Raising up on the cylinder head cover???

Hey guys, trying to get a buddy straightened out on his 2005 TRX500 Forman. Story behind this is that it sat on a farm for maybe 10 years. A friend of his added a new cylinder head and cylinder and also a new timing chain as well. I'm hoping not to go behind and tear this thing down again after his buddy did all that work. A new piston and rings were installed also. The word IN on the piston is facing the pushrod side of the motor. When trying to fit the head cover on the motor and slowly pull the recoil, the cover wants to raise up??? When I had replaced a grizzly 660 top end, Everything was new and fitted for the new cylinder head a cover. So far I have looked into the cam followers just to make sure there was no dirt making the pushrods seem taller, thus bringing the cover up from seating properly. The cam followers have new oil and seem to be seated properly. The lobes of the cam look very good. Slow rolling the recoil once again putting pressure on the followers, I can feel them moving. I'm waiting on a new set of gaskets now for the cylinder since it couldn't be saved. Any input would be awesome...thanks