Simply add a new save catagory with the save bonus raising as levels raise. d4 hit dice characters would use the poor save advance, d6 and d8 use average, and d10 and d12 would use good.
There is thread somewhere in the d20 section detailing how to convert creatures I don't have it handy at the moment but it works well.
Good Luck, I have personaly converted almost all of my d20 games to a mixture of M&M and Spycraft rules with a few bits an pieces gather from here and there, and it has made the game oh so much better. they ar quicker, smoother and the rules no longer seem to get in the way. even the rules lawyer in our group has stopped being so anal retentive.