You can't get the allignment marks to fit? Then it could be the flywheel/generator that has gone loose. I don't know if you have had it dismounted?
From time to time they get loose. It needs Locktite and the correct torque to fit it again. The washer behind the flywheel can be tricky as it drops out of position when you position the flywheel on the cranck. Use a dap of grease to hold it in place and inspect it carefully after mounting before you apply the full torque to the nut. /H2
Thnx ,,, careful of cylinder drop . appears to be timing,,,can't get crnk , vert., and horizntl to all line up with vert. at TDC ,,,, really frustrating . done alot of work getting it running again ,,, then this . any suggestions GREATLY appreciated . A.L.