OP, I think it's fair to point out to Jay that Logan is being his old manipulative self again, and quite possibly trying to break you up by inviting Jay to the wedding without you. Tell Jay that he has to make up his own mind about this, but if the roles were reversed, there's no way you would agree to be Rose's maid of honor if your BF was excluded from attending the wedding.

If he doesn't already know, you should also tell Jay about how Logan used to flirt with you before you and Jay met, how he would pry into your personal life (based on snooping Rose's phone) in ways that made you uncomfortable, and how in your opinion he's never been a very good BF to Rose. Remind him about all the times that Logan has messed with him personally, and about how peaceful the last six months have been without having him in your lives.

Finally, tell him what (if anything) will break your relationship if he decides to be Logan's best man, and Logan manipulates him into a compromising situation with one of the bridesmaids or some other woman - which he will likely try to do. You're not being a crazy controlling GF by explicitly stating your own relationship boundaries, and then following through if they are violated. If strict monogamy is one of them, make sure Jay understands that before he accepts Logan's offer.