Hi I did just this conversion started with a m600 dark 2000 fitted a 1997 900ss engine problems were
1/ single phase charging on SS sorted by just connecting to two of the where's on reg rec
2/ needed m900 exhaust headers as they are a different length
3/ needed oil cooler and hoses
4/ different neutral light switch wireing needs mod
5/ carbs are same size but different jet sizes use 900 dynajet kit
6/ need m900 inlet manifolds
Engine bolts in no probs if you want any advise just ask done lots more mods aswell

Cheers mate.
My original post was more than 3 years ago, since then I sold the M600 and bought an M900... I wasn't as adventurous as you.

I'm sure your offer of advice might help a fellow ducatisti though, thanks for that.