i've got both engines on my workbench right now for my own project. i'm using 550 cases with a 650 top end to achieve a 718cc overbore and keep the kickstart. the only way you could use the 650 trans with the 550 kickstart is to use the 550 1st gear. i've assembled it this way, when i was trying to figure out which gears to go with, but i decided just to keep the entire 550 gearing.
first of all, you either have to use 550 cases (which requires using the 550 charging system), or have the opening machined into the 650 cases and the support post welded in.
you have to remove the 650 gears from the mainshaft. 1st gear is integral with the shaft, requiring you to use a 550 mainshaft. reassemble the mainshaft gear assembly. then, disassemble the countershaft replacing 1st gear with the one from the 550. now you have a 650 transmission (sort of) that will align with the 550 kickstart. oh yeah, you will also have to use the 550 clutch press plate to allow the 550 clutch cover with the kickstart hole in it to fit.
piece of cake, right?