The d20 guide states that you may not change the meaning of any defined terms. The standard abilities are all defined terms. However, the ability definitions given in the d20 guide do not specify game term bonuses.
Technically, it looks like you might be able to change the game-specific bonuses of the "defined term" abilities without changing their defined meanings.
I guess the real question is, why would you want to do this? If you use terms which are already defined within the game, almost everyone who reads your product will have pre-conceived game meanings for these terms which you will have to overcome. This will just cause confusion and negative reactions to your rules. If you want the terms to have different game rule meanings, why not just use similar-but-different terms?
-Dave
(not a lawyer; giving opinions, not legal advice)