Frank,
One thing you should check is if there is a bind in the engine. Put a few drops of fuel in the venture. Flip the engine so the fuel loosens it up, take the plug out but leave the muffler on. Slowly rotate the engine through a full rotation (best is if you can also take the backplate off so there is no base compression holding it back). Feel the shaft as you rotate through the up and down stroke. A bind can develop because of varnish, case distortion from muffler bolts or head bolts. If you feel the bind, remove the muffler and test again. If still binding go around the head an loosen the bolts one at a time 1/8 turn, test after each bolt is loosened. If you find one that cause the bind to go away, mark the hole, check if the bolt is rubbing the side of the hole in the head. If so remove the head and run a drill one size larger then the existing hole (I do this to all the holes in my Fox heads). If it is not rubbing take the bolt and put it in a drill and file down the head (if you have replaced the factory bolts with socket heads you will need to file them all down to match the factory bolt diameters or they will rub on the fines and seat and distort the case causing binding) If still binding pull the piston/cylinder and de-varnish. For this I have used a small piece of Scotch Brite green pad with a little light oil. Run the pad up/down the bore with a twisting motion, also clean off any varnish spots on the piston. Go slow and test so the piston slides up the cylinder smoothly with no bind. While you have the P/C out check the shaft rotation for rough spot or binds, not normally an issue but I guess if the shaft is bent you would feel something as you rotate it. If bent you might need to replace the shaft and case (likely not worth it).
Best, DennisT