Tuning modified setups is a trial and error process if you don't have all the fancy gadgets a dyno shop does. Went down lots of dead ends with the 750 triple project. It was flat in the middle too. It would rev to a certain point then begin making a blubbery sound with no throttle response. Went up in jet size, got worse. Went down in jet size, Saw some improvement. Got to a point that things were real close, but no adjustment would smooth the trouble spots. That's when plug chop readings came to the rescue. Even with the K&N pods the bike was over fueling at WOT. Thanks to the forum I understood a bit about manifold air pressures. A couple of minor mods to the mikuni CV carbs helped to deliver the extra air and keep the intake pressures up. The bike runs smooth.
Well, as smooth as a non-counterbalanced 3 cylinder can.
On the other end, my 550/4 used to run up to about 2/3 of the throttle before there was no more response. It didn't blubber out, just wouldn't go any further. That's a sign of under-fueling. Rebuilt the motor and restored some carbs with bigger 105 main jets, and it's got a little more spunk now. This is with a stock airbox, 650 cam and port contoured intakes.