Yay! Oh, I'm flattered, that I'm the person for crazy crossovers X3
Hehe, I love the ones you have so far - I especially love Machi as Mithos because I always imagine Machi to be him because of the blonde-looking-like-a-girl thing they have going on.
And Raine as Ema is perfect because she gets annoyed and throws things at you XD
Okay, so so far on the AJ side, you have an Apollo, Trucy, Kristoph, Klavier, Ema, Thalassa, Machi and Valant.
And you have Lloyd, Genis, Kratos, Zelos, Raine, Martel, Mithos and Yuan on the ToS side.
I think that makes Regal Phoenix, then. You need a Phoenix, and Regal has the slightly-ragged appearance, as well as being a father-figure for Lloyd in the game and going through a hige fall-from-grace thing. Playing the piano with handcuffs has gotta be pretty hard, mind.
I think Presea works well as Vera, since they're both absolutely adorable, and when you intitally meet them, they're all quiet and withdrawn, but get more open and likable as you get to know them.
Dirk would be the Judge. I would love it so, so much if the Judge spoke with Dirk's awesome, awesome voice.
This might be one of those Things That Should Not Be, but I can't help but think Colette would make a half-decent Gumshoe. They're both optimistic, well-intentioned and have people they really admore, but they're slightly useless most of the time. X3
Sheena... uh, I'm thinking maybe Olga? Except kind of in reverse; Sheena initally meets you and wants to kill you, but you find out she's really a nice girl trying to do what's best, while Olga's sweet and shy at first, and then turns out to be a ruthless gambler. I can't think of anyone else for either of them (the only other female AJ characters are Alita and Little Plum, and she definetly doesn't match either of those o.o).
Uuuh, Brushel could maybe be the Wonder Chef because he shows up all over the place for no real reason?
Pronyma would have to be Alita, I guess, because she's all evil and such, Daryn could be... Forcystus? He's the Grand Cardinal I imagine would look best with an electric guitar XD
Hotti can be the Mayor of Iselia because he's creepy and I don't like him :/
And that's pretty much everything I can think of XD Hope I helped~