Firstly mate, Yes, if the float height is wrong it will just flood petrol though the airbox. Do you have a manual, if so strip, clean and reassemble the carb to the factory settings.
What year is the bike, and what year is the newer engine. When changing over the electrics did you fit a newer CDI unit. The fitment changed around 1997, I think. Now I dont know if the electronic brain inside the box changed but the CDI is not functioning correctly your bike will do everything you suggest in the opening paragraph.
As I say Im not sure if the internal of the unit changed at the same time as the wiring fitment, and indeed the new enging mapping may well have the same advance, retard curve of the auld engine, but summie else to think about once you sort the carb.
seemingly 50% of all carb issues are electronics and visa versa