i had a 03 CR85 and it was indeed rather 'abrupt' in power delivery but not terrible.
the '05 and up were much, much better. my meager .02 ?
You're right and that was partially because of the round-slide carburetor. In '05, Honda started using the Keihin PWK28, flat-slide carburetor.
As for the original topic, brakes, suspension and handling are top priorities. A good suspension set-up will get you better lap times and a better braking set-up will get you far deeper into the corners. Stiffer springs will get you started on the track, but realistically, the shock needs to be revalved and the front-end should be converted to a cartridge system. Sort those out first, then tinker with the engine.
Time and time again, I've seen guys with a well sorted suspension show the guys with a well sorted engine the fast line around the track.
Also, using a set of warmers on a set of GP slicks is mandatory. No amount of warm-up laps will soak the carcass with enough heat to make them stick and conform to the asphalt properly. As it stands, it takes 30-45 minutes at 170 degrees to completely heat them with warmers.