you need to change the GENERAL from ALT to Y. That way, all games that used ALT will be Y.
No, not for the games he's talking about: those games have the input key hardcoded in the source, and neither the ctrlr ini nor the "Input (general)" can change it ATM.

Tyweed, if you are using the ctrlr ini files like it sounds you are, or "input (general)" like Thenasty suggests, you can:
go into each game, go into the "input (this game)", go to the player1 button2 input, press enter (or, if you changed it, what you have mapped to "UI Select"), then press esc (or, if you changed it, what you have mapped to "UI Cancel"). This will force the game to use the default input instead of the input as hardcoded in the source.