Tough week, car broke, rushed out on my bike to rescue her, after the repair, in a hurry forgot about the disc lock and to make it much worse I had moved the bike backwards so had a good run up and really crunched things. Had to really muscle the broken lock off, the only silver lining I suppose was that I had my good tools with me. Raided spare YZF for parts, so maybe in the new year it'll be a pinky? Also (if anyone remembers) that H100 I'm rebuilding, ya, neutrals not where it's supposed to be...
If I can offer any advice, it may help to shift the bike's gears up and down while also spinning the output shaft by hand, do that a few times before you torque wrench the cases together. That's saved my bacon every time there was a misalignment.
Good luck, sorry about the fairing.