With the changes to skills etc, there's obviously going to be some hammering to make things fit properly...I've got some characters with non-core classes/prestiege classes in my game I'm converting, and I don't see any signifigant issues, though I've had to make one house ruling already and am debating another...
1: Monk gains Martial Lore as a class skill (and Martial Lore can perform Concentration things as well, applies to Tome of Battle)
Kensai prestiege class requires 2 Class ranks Martial Lore or 4 non class ranks, gains Martial Lore as class skill
2: Bear Warrior grants an additional rage/day at 7th lv. Friends and I are debating, does Bear Warrior grant full Rage Point progression, or does it alternate between Rage Points and giving a new Rage Power? The ability to turn into a bear is essentially its 'rage power' inherent, hence not going full WITH rage.