It'll need air inlets at the front that are equal in area (at least) to the area of the cooling air inlet on the front of the engine. Without this, the cooling fan will attempt to recirculate air around the engine, drawing hot air from the exhaust. This will cause the engine to run hot - likely much too hot, resulting in a dropped exhaust valve. The hovercraft community went through a phase of this when people messed about with the cooling of Briggs engines in the early naughties. It must have plenty of cool air coming in from the front, and I would strongly recommend measuring the head temperatures before and after the mod, so you can tell if you have enough air coming in.
Also worth doing is measuring the thrust before and after the change, as it will reduce airflow into the fan. Probably see a 10-15% reduction at a guess, although I have seen oversize engine covers cause a 25% thrust reduction. As long as this is tolerable then nothing to worry about, but worth knowing so that if it refuses to go over hump you'll know why.
Ian