I have put this engine in and out of the tractor twice so far , it does start now put seems like I am off a tooth on the timing . when checking the t mark and s mark on the flywheel with the opening and closing of the points things aren't lining up

 

Just line the marks up on the cam and crankshaft, and you're done. They are helical cut, and look odd going together, but as long as the marks line up when the crank is all the way in, you're gold.

The points open and close every other rotation of the crankshaft. Are you sure you're on TDC of the compression stroke when the proper mark is lined up in the hole? I can't remember off hand which is which, but the timing mark comes first, then the TDC mark.

The point gap is just a round about timing setting, odds are the points will have a different gap once the timing is correct.

 

I think I read that the t mark was top dead center and the s mark was for spark