George,
It looks as if you will need to draw the pinion off of the stub shaft that drives the magneto, then refit the magneto with the drive dog keyed to the armature. With the mag correctly timed, the pinion can then be refitted on the stub shaft. As the cam followers fit either side of the camwheels, it is pretty well impossible to upset the valve timing while you are doing this, but make sure you have the mag timed to the correct cylinder. To do this, remove the FRONT HT lead from the magneto and check that you can see the brass segment on the slip ring when the points are about to open with the mag fully advanced. Turn the engine forward until the REAR cylinder is at TDC with the valves rocking, turn the engine backwards about a quarter of a turn, then forward again to the correct timing point (about 40 degrees BTDC), then refit the timing pinion.
Hope this helps,
Regards,
Eddie.