Hi chris,
I've seen your project on the 125cc forum, but weren't aware your carb was giving you grief. I agree with the general consensus that it's better to set it set up properly on standard before making any adjustments. As I'm now the (not so)proud owner of a Crono, which is a dog to be fair, I can compare the carb on it with a spare GFR unit I've got sat around. I'll post pictures if you wish .....
Apart from the silencer's looking a bit different, I can't say for sure whether a GFR unit on a Crono set up, or vice versa, would make any difference. I would assume there may be subtle differences otherwise Gilera wouldn't have gone to the time, effort and cost of redesigning it for the GFR.