Especially since MC sets up things that are later picked up in X-Factor. You could start with pages from Uncanny 492, then most of X-Factor 25 (I honestly would be okay with cutting out PAD's pages of Wolverine finding Voght, and other stuff), then from next issues take those in Washington with Rictor (although it is getting heavy on New X-Men as it goes on) and those with Layla and Madrox in the future up until X-Factor 27 I think when Madrox Prime comes out of the coma. Half of those wouldn't be by PAD, but at least the story would be fluent(ish), and then next arc of X-Factor follows the Purifier that Rictor fooled, and Layla one-shot continues her story and they're both in the vol. 2 too.

Having parts of the cross-over important to given book mostly separate from the rest of the thing is what makes X-Factor/MC unique case and I think it would work here. Wasn't not so long ago similar thing done in the Venom TPB?

Oh, and if we're talking complete complete, I think there was also X-Factor appearance in Friendly Neighborhood Spider-Man by PAD, but I don't know if it was a cameo or something bigger.