[Edit] I just realised I'm lookin' at my 550 parts list. Not sure if is the same, sorry just in case.
Was the kick start okay before you changed the lever?
I wonder if you might have used a hammer to get the new one on? Was the pinch bolt removed before you slipped it onto the spline?
If force was used, I wonder if the circlip (#43 in the pic below) hasn't been displaced and
shaft is too far in now? [Looking at that, I don't think it can happen. Sorry
]
I've never heard of the kick start pinion seizing on the shaft but who knows until maybe you get into it a bit further.
Good luck, I hope you don't have to split the cases.