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Are you single fire or dual fire? If Single Fire do you have the coil wired properly?
Also are you rotating the engine with the rear tire or kicker. If using the rear tire you should be rotating the tire the way the bike drives; the marks in the timing window should be going from the rear of the bike to the front.
Dual fire. I'm rotating the rear wheel in the the direction of travel and the marks move through the window from back to front.
Those timing marks are very sensitive. I know that I have chased my tail enough times because I had the proper Timing mark in the window exactly where I wanted it and then went on the other side of the bike to set the Timer plate without realizing that valve spring pressure and other factors moved the crank wheel where the Timing mark moved while I was going to the other side.. It will be helpful to have another person on the other side or to lower the rear wheel to try and lock the mark in place.
I do not rule out anything. If you haven't owned the bike since new, the crank wheels may have been changed from a different era or I also suspect the factory has used older crank wheels on occasion. Bottomline those timing marks are very sensitive and move through the window very rapidly. They are easy to miss. Using a straw to find TDC and looking at the lifter location is not going to lie, regardless of what is in the window. But again, once you have done that, lower the rear wheel and try to lock that crank position in place. Also having one guy on each side helps with that problem as well.
ETA: I know one time when I installed an Ultima like yours, it said I had to use a Gold color rotor, when in fact I had to use a Silver one (or vice versa, my memory is not perfect).
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