my bike did this at exactly the same thing when cruising along at 4500rpm. when i revved it up, through these revs and beyond whilst "getting on it", it was perfectly fine. Even a wide open throttle dyno run didn't show the problem, 'cause it was only at small amounts of throttle.
due to the bike having slip on's & a bmc air filter, it was running lean at, and around, 4500rpm. so i fitted a PC3 & got a custom tune, and the surging went away. the map i had done has 25% more fuel added at 4500rpm, at low throttle position (like you use when cruising).
if i was you, get it on the dyno and simulate small throttle cruising. my issues were at 2 & 5% throttle positions, between 4000-5000rpm.
2004 YZF-R1 Track Bike (the clunker)
Exhaust: Micron Slip-On's, Akropovic Y Pipe, Exup valve deleted w/ Graves servo eliminator.
Intake: BMC Air Filter & Factory Pro Velocity Stacks
ECU: PowercommanderIII USB w/ custom tune by Dynoverks (150hp at the wheel)
Bodywork: Doctor Race Glass, yet to be painted
Brakes: Hel Braided lines front & rear, Goldfren carbon ceramic pads, Motul 600 fluid.
Rolling on: Superbike Pro "track day" slicks.