I'll throw out my $0.02 to say that below 3500 RPM, the bike is difficult to tune for fuel. The rough nature is most likely a fuel issue or at least the majority of a fueling issue.
W/O a PC and aftermarket exhaust, the bike will run extremely rough because of incorrect fueling. With a PC, you can smooth it out but fixing smooth roll-on becomes difficult.
In most cases, jerky, rough or surging is caused by a lean fuel mixture. Adding fuel at the lower RPMs should help but since the RC is a twin, you have the two independent cylinders to try and tune which means it will be very difficult to manually fix without dyno time.
If you want, manually add some fuel in those lower rpms for both cylinders. I run the stainless yosh slip-ons and below 3500, my fuel map is adding around 10% in the various 2% - 5% throttle position cells. Above 3500, it removes 10%+ (-10%)
I run the PCV with autotune and noticed that the bike does not run smooth with an AFR above 13 in the 2% or 5% cells. Just my own personal experience.
If you do stepup to the PCV at some point, keep your PC3. There's a problem with the PCV and RC51 that causes an RPM bounce. Keeping the PC3 in and adding the 5 to it will filter the problem. (Do a google search for RC51 rpm bounce for more info)
Long story short, proper fueling at those low rpms should fix the problem.