I have a 93 fizzer 600. What was rebuilt? You might want to replace the spark plugs to CR9E´s. I recently replaced to these and they seem to accelerate alot smoother than before. Also, check the filters. Before riding, let it warm up couple minutes. Always use the choke to turn on bike each morning for first time. Try these, but I can´t really say what the problem is. It doesn´t sound like a transmission problem. Has the chain or sprocket been replaced. If so, they recommend replacing both at the same time so that neither one causes problems or loss in performance.
I just got a K & N air filter/ oil filter and will be using it on my bike w/ Yoshimura slip on. Can´t wait to see the increase in performance....hopefully. Good luck