the pro circuits will not compensate for a bottom end loss. Your intake velocity will be reduced, which will reduce the amount of bottom end the motor makes. The biggest thing is, you usually use a bigger carb, the higher the motor revs. If your redline remains low, like 9,000 rpm (pro circuits), then your motor will not fully utilize a big set of carbs. So not only have you reduce the low end power, you have not fully utilized the carb to its full potential. He stated he was going to change the pipes, so that will warrant the use of bigger carbs. However, the power curve a set of cpi pipes makes is ALOT different than the pro circuits. So be prepared for that.
Which mikuni carbs? Flatslides, rounds? TM, VM, TMX?
I run a set of Mikuni TM 28mm carbs, but I also like the Lectrons.