Oh, and one minor change I would highly recommend for part one, add the Marvel Comics flipping pages logo onto it. I for one really like that logo and it would tie it in with the other marvel movies better.
It would be hard to explain a few things between 2 and 3. Shadowcat is different, Nightcrawler is gone without explaination, but I guess those things are not too bad. I guess cutting out the Kity Pride reference from 2 and adding a simple "this many months later" subtitle between the 2 and 3 footage would explain things well enough. The hardest thing will be dealing with the death of Scott, which is what I would say ruined the film the most. I think for any reasonable fanedit, the whole Scott thing would just have to be left in. Moving the scene with Charles in the body of the man at the end of the credits might be cool to move before the credits.