The bike is a 1973 yamaha ct3.

The engine has spark, fuel, and compression. The timing is off by 90 degrees and I have no idea how to fix this problem. There doesn't look like there's any way to adjust it and these are all factory components...I must be missing something. Any help? Thanks.

Can you check to make sure the woodruff key is located correctly in the flywheel and crankshaft ? If you remove the flywheel nut and washers shine a torch up the end of the crank to see if it looks located right. If not you will need a flywheel puller to remove the flyheel.

are you sure you have the correct flywheel ??