before you start it!!!!! unscrew the inspection cover and make sure the altenator rotor and the groove in the cover are aligned! the cam should be in the horizontal position . at the same time. if your off just a tooth or 2 she will run badly if at all and could mess up your valves big time
. I had this happen
make sure your top dead center, both sets of valves should be equal, not one set up and one down. if not take the bolts off the cam sprocket then loosen the tensioner.Turn just the cam, not the sprocket( you will lose the bottom alignment!) tap a 2 X 4 in between the frame and the cam once you get it in the the lined up position at the same time the altenator marks line up.
.tighten chain tensioner,remove 2 X 4 and then put plate and bolts back.dont forget to put the inspection cap back in( dont ask how i know
, but it will throw oil everywhere)
sounds like its not top dead center, the head cover should fit right on if it is! good luck!