Tips for making things truly waterproof (to 50,000ft!)
1) Minimise things that pass into the potting, eg wires. Water finds its way down the interfaces between the potting and the wires driven by atmospheric pressure variation. Typically there must obviously be some connections but keep it minimised. Ideally the whole thing is submerged with just a couple of wires coming out.
2) Insulated wires are pipes that transmit water exactly to the most sensitive parts of the circuit! I've seen this many times in failure investigations. Try to avoid insulation passing right to the board.
3) If you can vacuum pot it then so much the better. Put the item in a vacuum chamber, pull a vacuum, hold for a couple of minutes then let the air back whilst before it cures. That'll drive the potting deep into the nooks and crannies.
The main thing I've learned over the years is its really hard to keep moisture out forever. You must either form a chemical bond, form a high pressure seal (O ring) or welded joint to keep it out permanently. But anything you can do is better than nothing!
Dunking coils in varnish is good, better if you gently heat the coil first (70 C is safe, I've done Briggs coils at 90C). Coils would really benefit from vacuum dipping, that will drive the varnish right into the laminations.
Ian