yeah, you sure are right pinhead. eric (mr. blasty) and i sat there and looked at the two sets of cases right beside each other after i tried the 550 cover on the 650 cases, and i swear they look exactly the same. but as you stated, the 650 cases are slightly smaller on the rear half of the alternator area.
so, back to plan A.
550 cases, alternator, and clutch basket. 650 crank and top end, and a mish mash of clutch and transmission parts.
i figured out tonight that i should be able to swap out whatever gears i want from the 650 or the 550. if i keep the primary gearing of the 650, i'll have the supposed benefit of it's better clutch. i'm actually thinking about using the 650 transmission with the 550 1st gear, so i can keep the kickstart, but i still want to figure out what the best combination of gears is from both bikes.
it seems that the easiest solution to keeping the gearing i'm familiar with in the 550 and still have the better clutch would be to use the 650 primary, full 550 gearbox, and then just adjust at the final drive to compensate for the lower primary ratio.