JZ,
I'm in the same boat here. Unable to find any docs on how to disable the Ctrl-F and Ctrl-R shortcuts. If you have found a solution since your last post, please reply with the solution. In the mean time, what I'm going to do, even though it pains me, is to map Fire to some button other than button 1 (Ctrl) in the emulator. I think I'll go with button 3 (space), which should not trigger any unwanted shortcuts in Stella.
Thanks,
-E.V.E. Games