Which part are you referring to? I am currently struggling with getting the cover off. It's like I can get it started but that's it.
There is a plastic piece that goes between the upper cylinder head/valve cover and the V section in the frame to keep air from the radiator from getting under the tank.
It could be caught on the lip of your cover keeping it from lifting very high.
Once I got all the bolts out, I had to do a bit of wiggling here and there and hold my tongue just right to get the cover off, but it did come out fairly easily.
During that process, I hit the T-stat housing though, and caused a leak, so I also replaced the T-stat and all orings in it.
Getting it back in place with the gasket in was a bit tougher. I tried forever without using any kind of sealant, but in the end resorted to a liquid high-tack gasket dressing which worked wonderfully.
On the coils, I dont know if we are talking about the same part. I thought you meant the rubber part that goes over the plug itself. Seems some other are thinking it could be the round rubber seal at the top.
For the top, I used the ones off my factory plugs...cut down I think, and left the round rubber ones off. They fit too tight for my liking, if I recall. Its been a while since I had the plugs out, but maybe I should at least pull the coils just to be sure I greased them and dont have a similar issue.