Hi
well something's wrong with your g3Config.C.... can you post it here?
To answer your first question: you don't have to recompile, you can change g3Config.C and SetCuts.C without any further steps necessary.
If you want to create data with different settings, you can also specify a custom directory in your macros for the g3Config.C and the SetCuts.C with a statement like
fRun->SetUserCuts(dir+"SetCuts.C");
fRun->SetUserConfig(dir+"g3Config.C");
with dir being your custom directory and fRun the FairRunSim* pointer.
Cheers
Felix