Too funny, I'm doing the same thing but without skipping ANYTHING and I'm up to just before Operation: Zero Tolerance. It's sort of hard to say what you should and shouldn't skip, as it sort of depends on what your goals are. If you want to have a solid grasp of X-Men history it's hard to ditch either X-Men or Uncanny X-Men, even if some of the stories are not that great. As said by someone else, Excalibur pretty much sucks and is relatively detached from what's happening with all the US X-Teams, so if you want to drop something I'd start there. Wolverine has some fun stories after the first 10 issues, but is consistantly uneven and you won't really miss anything important by dropping the title all together. X-Force goes back and forth, but is a fun history lesson in balls-to-the-wall 90s comics, so I enjoy it for the kitsch, plus it's funny to go back and see how obvious the Rictor/Shatterstar romance was in the mid-90s, even if never addressed directly. Other than that I'd recommend skipping just about every unnecessary 90s mini series and X-Man. You might also want to skip Cable, but I find it has a bit of heart that I enjoy, and often ties directly into X-Force.

Overall, reading through the 90s will be a labor of love. I'm glad I'm doing it, but the majority of it I would never, ever, read again.

PS If you're as close as you are the New Mutants and X-Factor, just stick with them. They both loose all their steam, but New Mutants sets up a lot and X-Factor gets awesome when Peter David takes over and stays mostly enjoyable after he leaves.