Thanks for the quick responses. I didn't start a new game after editing herostat! Duh, had no idea. I guess I was living in the dream that you could work around the 27 char limit by just editing it and dropping in whoever you wanted as you played through, but alas. I edited herostat again and started a new game and it seems that most of the glitches were fixed (Jean can now fly, as can Doom and Rogue, She-Hulk can lift stuff...ah, what a relief).
There was a sec where Rogue's power list/HUD disappeared, and one of Jean's skins was flying all weird, but maybe that can be chalked up to the experimental nature of modding (it was a New X-Men skin on the Jean booster).
Is there any way to have the game start with a different set of chars? Do Thor, Cap, Spidey and Wolverine always have to be in there?