got any photos? 

a prop screws through the air, this results in a push, but its not pushing air. this is why a prop is less efficient at no forward speed as it is literally trying to screw through the air. the best prop is open and unimpeded inlet so it has clear air to screw through. 
a fan is sucking in air and pushing it, which is different  to an open prop. 

if the top being up or down is affecting the amount of air getting to your lift fan, you have an aerodynamics issue, the air is likely sticking to the curved surface of the roof, like a wing (coanda effect) when the air exist the roof, it will be a lower pressure and turbulent, if your lift fan is in this low pressure turbulent zone it will run less effectively, as it needs to do more work for the same differential pressure from inlet to outlet. 

Al
Here is something on which to ponder.
I'll try and keep it short, so you don't think" oh what's he on about".
When I designed the cowlings for the rear section of Kermit.
A lot of thought went into the way that the airflow was going to be used.
Let me discuss the bit that you have changed.
Fans and propellers are greedy things. They will grab air from anywhere that is easy for them.
They aren't bothered if they are taking someone else's essential supply.
On a Sev there are 3 fans trying to get their share of the air.
1 Propeller
2 Lift fan
3 Engine cooling fan.
My thoughts were to give each fan as smooth an airflow as possible. And to make it that the weakest got its share.
The top panel ( The one that you removed ) did two jobs. It smoothed the air into the propeller.
And I made a NACA style duct to direct the air into the engine cooling fan..

What you think you have done is make it easier for the lift fan to get air. In doing that you have alleviated the problem you think you have with lift.
BUT.
What you have actually done.
By allowing the lift fan to get air from anywhere it likes.
You have taken away the NACA duct that feeds the engine cooling fan with smooth air.
You are making compete for air with the lift fan........the cooling fan is never going to win.
Can the engine cooling fan get enough air in oeder to keep the engine cool.
i don't know that, and neither do you.
The only way I can think of to monitor it, is to fit cylinder head temperature gauges.
I really don't want you to destroy your engine.
Everything I did was calculated using the very best of my limited knowledge.
Taking bits off Willy Nilly to fix a perceived problem, whilst not considering the problems you may have caused in doing that. Makes me worry.
John, Ian and Steve have expertise and experience far greater than mine.
It would definitely be wise to speak to them.

Originally you said the plough in was going downwind.
Now you are saying it is caused by the hood being up.
The lift fan picked up its air from the sides and back.
I can't see how it would be possible for the hood to disturb the airflow in that area.
I used the craft with the hood up and down ( although with no side panels.
I couldn't feel any difference.
But it never, ever ploughed in.

HI Ronnie,

The problems I was experiencing was always with the roof up.  It didn't matter if the wind was light of heavy, the craft didn't have the lift to stop the nose ploughing.  It also struggled on land with the roof up as would frequently hit small boulders on the beach.  Since removing the rear cover the craft has operated much better with the roof up and down.  The craft gets onto lift quicker now and maintains lift at lower RPM

Hi Al
I'm in Oban and it's pretty calm here.
Is the wind higher up there?
As the problem you seem to have, that strangely I never had over the many years and hundreds of miles of operating that craft. Also carrying two people a big dog and a very, very heavy toolbox.
Is when you are going downwind in a strong wind. 

Today I was able to play on the loch after fitting the new guard.  Pleased to report that the hovercraft showed no signs of wanting to plough even with the RPM at around 2500.  At one point we did touch 30mph, but I soon dropped the RPM, as I was purposely trying to keep the speed at around 20mph.   Initially we headed for the river Carron, but it seems it wasn't where it was supposed to be.  From there we headed to the island in the middle of the loch and had a wander on the island.  From there we headed down the loch to the beach at Ardnarff, again a short nosey, before heading up the loch towards the avalanche shelter, then across to one of the islands, as we spotted seals on our way down the loch.  From there back to the launch site, as I had to be back by 16:00.  

Well done. I'd like to see a photo or two of your rear end. 

Well done. I'd like to see a photo or two of your rear end.  

I finally was able to get back out on the loch today.  The day started badly with the electric winch not working.  Battery only had 10 volts in it, so looks like one of the cells has given up.  Tried a different battery & winch still not working.  After investigating it, looks like winch motor has packed in, so new winch ordered.  So pleased that I fitted a manual winch as a back up a few weeks ago.
Anyway, we finally got down to the loch after lunch.  First run up the loch with a very light breeze behind us, was with the roof up.  I tried to keep the engine RPM around 2500.  I reached a speed of around 22mph.  I could feel the craft wanting to plough, but it didn't.  Once we reached the beach at the north end of the loch, I lowered the roof.  I then flew to the island in the middle of the loch and after a brief stop on the island for a few pictures, we started our journey back to the top of the loch, but within a few seconds of pulling away from the island we heard something go through the propellor.  So I immediately, headed back to the island and switched off the engine, to investigate what had happened.  Not sure how it happened, but the starboard side of the safety netting had got caught in the prop, and had wound itself around the prop hub.  Only thing I can think of, is that a couple of the cable tie holding it to the prop cage had let go, allowing part of the netting to get caught in the prop.  Luckily no damage, other than the netting needs replacing.  Lesson learned, change the cable ties holding the netting every few months.
We headed back to the beach at the top of the loch and the craft felt happier "if that makes sense".  Once back on the beach, I then removed the rear center cover and headed back to the island with the roof down.  Immediately the hover felt more nimble regarding lift.  The craft popped on to lift noticebly quicker than the previous two flights.  This time I flew it around the rear of the island.  I still tried to keep the RPM around 2500.  Once around the island and heading back to the beach at the top of the loch, I noticed we were travelling at 32 mph without even trying .  We could feel the craft trying to dip its nose, but immediately divider skirt doing its job, keeping the nose up.  Once we got back to the beach, I put the roof back up and left the centre cover off.  Again the craft was working as it should.
For the flight back to our launch site, I once again put the roof down and left the cover off.  Again it flew very nicely.
I'm now going to buy some stainless steel mesh and make a new centre section for the rear end.

[just]

29mph downwind in a 15mph tailwind is too fast to retain adequate control (and may be at/close to the lift system pitch capacity in anything other than perfect conditions).  In a 15mph tailwind I'd be controlling speed to 20-22mph max. or if it soft-ploughs (telling you speed is too high) changing course to an angle to waves/wind.  Clearly the front compartment was unable to maintain enough flow/pressure.   With no warning it indicates a failure of the skirt or lift system.  Pre-flight checks are essential - particularly on the skirt contact area (even a small hole/cut can cause significant drag).  Possible damage on the front bags causing scooping/drag combined with excess speed and a tail wind produces significant down force on the nose - maybe overcoming the cushion pitch control?

You can easily check the nose up pitch control force available using a spring balance and a bit of rope.  Attach the scale to  to the tow point with the rope on the other end hanging down to a few inches from the surface.  Disable thrust and run the craft at full lift on a smooth surface.  Then stick your foot in the loop and apply weight until the bow skirt just brushes the surface.  You should get around 18-25Kg reading.  That is the total amount of force available to keep the nose up - compensating for thrust and craft load imbalance (driver and whatever is upfront) trying to push the nose down.  The force is pitch rotating the craft around its CofG.  The lever principle means you need less force the further you are from the CofG.  If the force is too low then the skirt trim is wrong OR too much weight too close to the nose.

The probable cause is something has changed (as was said below) - AFAIK the craft has never behaved that way before.

What is surprising to me is the description of hard hull contact with violent deceleration. The Sevs hull is designed so the it does not do that - the 15 degree minor plough plane does the magic there. Regardless of the state of the lift system it just shouldn't do this! Even if the power is cut in an emergency it should never submarine the bow. The plough plane is there to "skip" over the water and prevent the bows from submerging.

A minor plough in where the craft decelerates gently is not uncommon when flying directly down wind. But this will never unseat a passenger.

Are you sure the underneath is all to plan and is in good condition? Is the divider skirt ok?

The last time I checked the divider was OK, I didn't check it on the trailer, but perhaps something happened to it on our return trip.  Fist thing I checked when I got back ashore was that the brake flap wasn't stuck open.  The lower hull was built to plan using a jig, so I know bottom half is correct and true.  When I get back from holiday, I'll check the divider skirt, but as far as I'm aware, I haven't snagged it on anything

What is surprising to me is the description of hard hull contact with violent deceleration. The Sevs hull is designed so the it does not do that - the 15 degree minor plough plane does the magic there. Regardless of the state of the lift system it just shouldn't do this! Even if the power is cut in an emergency it should never submarine the bow. The plough plane is there to "skip" over the water and prevent the bows from submerging.

A minor plough in where the craft decelerates gently is not uncommon when flying directly down wind. But this will never unseat a passenger.

Are you sure the underneath is all to plan and is in good condition? Is the divider skirt ok?

You need to confirm any the issue first before randomly hacking around with the craft.  Next time it does it, stop (on the water) and put the roof down before continuing (unless you test during the exact same conditions its pointless).  Then remove the cover and try again.

Exactly what happens and under what conditions?  The video shows minor chop (about 6" I'd guess with no noticeable craft pitching/rolling - in other words well within 'normal' operating conditions).  Wind speed will be the difference between upwind and downwind craft speed x 1.5'ish.  Is the 'plough-in' progressive (nose lowers slightly during each successive wave impact), hard (water hull contact) or soft (braking)?  What speed before and immediately after?  Does it happen at 45deg (or 90 deg) to the wind or only when directly astern?

Assuming there is no skirt/lift system damage since the last time it was used (you need to check EVERY time to be sure) then there is no inherent reason why a known working craft should  behave this way.

Wind was pretty much directly behind,  We were doing 29mph (2800 rpm) then hard hull contact down to about 5 or 6mph, water up over the windscreen.  I tried keeping it at 3200 and opening the brake flap a fraction, to try and keep air pressure up and use the partition skirt to slow the speed, same result hard hull contact and down to a near stop.  It ploughed several times last time out all heading down wind.  Some of the plough ins you could feel happening, so I tried giving full throttle but that ended in the same result.  

As I said before, all the lift issues have been with the roof up.  Even transversing the beach it struggles to maintain lift with the roof up, but doesn't have a problem with the roof down.  It's as if the air is robbed from the lift fan.  "Perhaps I'm imagining it"  
I have removed the centre section of the cover now, as only 4 thumb screws to remove.The lift fan is now visible from above, so shouldn't be restricted.
I'm off on holiday tomorrow until early June, so won't be able to test it until I get back home. 

You need to confirm any the issue first before randomly hacking around with the craft.  Next time it does it, stop (on the water) and put the roof down before continuing (unless you test during the exact same conditions its pointless).  Then remove the cover and try again.

Exactly what happens and under what conditions?  The video shows minor chop (about 6" I'd guess with no noticeable craft pitching/rolling - in other words well within 'normal' operating conditions).  Wind speed will be the difference between upwind and downwind craft speed x 1.5'ish.  Is the 'plough-in' progressive (nose lowers slightly during each successive wave impact), hard (water hull contact) or soft (braking)?  What speed before and immediately after?  Does it happen at 45deg (or 90 deg) to the wind or only when directly astern?

Assuming there is no skirt/lift system damage since the last time it was used (you need to check EVERY time to be sure) then there is no inherent reason why a known working craft should  behave this way.

Hi, Al, what was the estimate on the tail wind speed you experienced?
My craft does not like strong tail winds, I sit as far back as possible and move anything possible to the rear. Mini plow ins occur with strong tail winds exacerbated by necessary lower throttle settings to keep speeds down.
I'd secure anything of significant mass in the craft so it can't move forward should a plow in occur.
This craft didn't appear to have plow issues during times that I travelled alongside it although that doesn't mean that it has developed an issue that has changed the handling characteristics.

Hi Steve, xc was saying 7 to 9 mph wind, but it was probably 12 to 15 mph. There wasn't any white caps on the water, so less than 20 mph   
I've had the same issue 3 times now, even in light wind.  Only common factor has been the roof has been up. Haven't had any issues with the roof down into or down wind with speeds in excess of 30mph.  I'm looking for a way to test the air pressure/flow under the craft, with roof up and down and with the covers on / off, into and down wind. This will prove one way or the other if there is a difference in air pressure / flow

Hi, Al, what was the estimate on the tail wind speed you experienced?
My craft does not like strong tail winds, I sit as far back as possible and move anything possible to the rear. Mini plow ins occur with strong tail winds exacerbated by necessary lower throttle settings to keep speeds down. 
I'd secure anything of significant mass in the craft so it can't move forward should a plow in occur.
This craft didn't appear to have plow issues during times that I travelled alongside it although that doesn't mean that it has developed an issue that has changed the handling characteristics.