I've got a '93 with the same V&H SS2R system, 4 into 2 into 1. I also have a Dynojet kit installed. I have no problems as you describe. The hesitation and surging are signs of a lean mixture. Go throgh your carbs as descibed above and make sure the pilot mixture screws are open enough. The screws on the bottom front of the carb control volume only, not mixture.

 

Is the gearing different between the 90 and 93? I took my 1990 out yesterday and 45 MPH in sixth gear was only 2,600. Also, if the piston/diaphrams in the carbs are not squeeky clean, the needle doesn't rise smoothly out of the main and can bog.

 

Thanks to everyone for your responses. Looks like I need to get a service manual and start checking things out.
The cbr owners manual recommends shifting from 5th to 6th at 37 mph,
but just to set the record straight, I'm not doing a lot of riding in 6th gear below 3k it's just that the low
rpm stumble is more pronounced there than in any other gear.