I threw a rod on this engine and had to replace it. I also put new rings in & lapped the valves. I could not start it so decided to look further. I lined up the two dots on crankshaft & cam shaft with both valves closed but the piston is not at TDC. On all videos that I have seen the piston is right at the top of the head. Mine is about 2 inches from the top. What did I do wrong or is that OK with the two dots being right on ? Thanks.

Hi,
It may be that you have a line-up mark of a beveled tooth on the cam(some do.) Another check is to move it to TDC after assembly and check the position of the magnets in the flywheel to the legs of the armature. The magnets should be slightly clockwise past the armature legs. Engines do not assemble at TDC since the ACR would be in play and could be damaged.
Peace,
Clarke