Welcome to the world of yamaha, where the quicker you learn your T's and X's the better off you are. In the before time it was all 6m6. this is the 650 stuff. An indestructible little torque machine with no balls. No matter what superjet motor you have you have a 6m6 crank, they never changed it. Your 6m6 electronics are swappable with x electronics. While plug in and play, a 6m6 cdi limits rev lower than the x motor outputs. In 1994 we get the "x motor", outside dimensions are basically a 6m6, but inside everything is bigger and better. (same crank though) So 6m6 and x stuff is freely swappable and the rev limit of a 6m6 cdi can be modded (if you feel its worth it). all exhaust stuff is bolt on and go, the x internals are just bigger.
Now yamaha drops T on us. The superjet gets T/X motors, the couches get T/T. On the bottom end, including electronics, T stuff is its own thing. Flywhee, stator, cdi (they changed a plug from male to female or vice versa) On the superjets they kept the X top end cause it comes on at a lower rpm. But the bottom end is now dual carb, the cases being highly sought and cost alone what an entire motor costs 7 years ago.
From the standpoint of exhaust, 6m6/x cylinders are completely different than T cylinders as far as how it bolts up. I hope this makes sense, please correct me on any wrong information.