I've used the XSeries II for a few years now, sorry I can't help with the manuals - there are usually some fairly basic manuals included on Thermo's install CDs, but beyond that they don't seem to be very forthcoming with them.
My experience is that, as with a lot of modern mass specs, the instruments need regular servicing from someone who knows what they're doing because some obscure part or other is always wearing out or going out of alignment - though to be fair we do use them pretty heavily. Depending on your technical prowess and budget, it might be worth forking out for one of Thermo's service contracts. They seem to much prefer working with people who are already on their books, and they do seem to give their money's worth. Or rather, they do a good job - I'm not the one paying!
On the other hand, the Xseries is very modular and probably easy enough to maintain if you can get hold of the parts and instructions. We're in a fairly remote location here, so we've often had the engineers post us parts and talk us through the repairs, which tend to be easy enough for anyone who can wield a screwdriver.
Edit: Agoo, I've sent you a suggestion about the password.