Very helpful that you ruled out vac leaks.
Although there are different schools of thought how to best go about tuning, I prefer "top down"... that means, get the mains close to dialed-in first, if possible. That can save unnecessary tail chasing, as different pilot & needle combinations can compensate for sub-optimal mains, to a surprising degree. And that can cause unintended consequences.
I don't recall what the fuel height is on my bike, although it is lower than OEM spec; I also use the sight tube method to verify actual fuel height. The above said, I doubt that is the source of the surging.
I suggest using some tape to mark your throttle twist grip, in 1/8, 1/4, 1/2, & 3/4 increments. You might be amazed at how little throttle is used JRA (just riding along). At any rate, take note of the specific throttle position when the surging issue starts & stops.
Have you pulled the float bowls to check for sediment? If not, I suggest doing so. And pull the pilot jets to make sure they are not partially occluded. If those jets are suspect, replace them. They are small enough to be easily damaged unless they are cleaned by someone with the correct knowledge & tools. To check if any of the other pilot circuit orifices are occluded, the carbs will need to be pulled to do it right, so just stop there for now.
I suggest not pulling the shims until you also have the larger mains on hand. Then, pull the shims & install the larger mains. Go test. Better or worse? Report your findings.
