might be something as simple as carb set up or timing, check all the basics first then look at the pipes, just bought myself a colortune off ebay for helping with jetting my Mikuni. wouldn`t be butchering them pipes too quickly. try a stock aircleaner.

usually use loose bottom and mid range when you run drag pipes ?? maybe they are flowing too much ?? rather than not enough what are they like up top in the revs if they are good in the topend then they most likely are too open ?? just food for thort ? if so you need to rejet the crb for more flow maybe ????