Hiya! Thanks for the comments. You couldn't post in Loopholes because it is in the completed fic section, which nobody can post in and only staff can move things there. Let's see about those questions...
Some of those things were red herrings, like how Sally looked like Darkrai. She's albino because Giratina gave her protection from the time freeze situation in order to be born and grow up.
Darkrai turned into a Skitty when the Palkia attacked him in the dimensional hole, yes. So you are right with there being two of them around. And with the Eclipse Robe in possession, he can turn into a Skitty and back whenever he wants; that gets around his problem of not being able to make friends. Manaphy knew him to be Kip for exactly why he said so: because he wanted to teleport to Kip. That, and Manaphy has some powers of innocence that nobody knows about.
Kip met Sally at the recruitment meeting. Any time 'prior' to that (due to time travel) is when he's Darkrai.
Sorry about the brainaches! I like that kind of challenge in writing. Thankfully, my other stories here aren't as bad about loopholes and confusing stuff. Well except for the Celebi origin story Bamboo and Cherry Trees. Because that delves into alternate dimensions, it's actually worse...