Try using a longer link pipe, or remap the bike to take care of fueling at low load.
^^This definitely helped my throttle/surging issues when I was trying different 3/4 system exhausts for my Gen V. The shorter the link pipe/muffler the surging and jerkiness was more prominent, especially when I owned the SC Project CRT setup. However when I changed over to the Akra link pipe w/the Akra "long" exhaust my bike ran just as smooth as it did when the bike had the cat and stock exhaust installed. I no longer own either of these setups since I'm running a Brocks Predator 3/4 system and guess what.....there's surging to a certain degree, however not as bad as it was when I owned the SC CRT.