I installed a jet kit in my 96 Daytona 1200 and it made a huge difference. I had a flat spot around 4,000 rpm that lasted till 5,000, the jet kit cured that. The kit I used was from K&N specifically for my model bike. It came with two sets of jets, one for stock and one for aftermarket exhausts. No guess work. The only drawback I've experienced is about 5 mpg loss in fuel mileage.
You said you had the carbs tuned. What was done besides having them synchronized? Were the pilot air screws also adjusted (2-1/2 turns out works best)?
Even if both were done your bike could benefit from a jet kit but that may not be all... How many miles are on your bike? Has it ever sat for several months without being ridden (ever in it's life)? Have the carbs ever been rebuilt?
To see what's involved
click here.
I suspect your carbs may need to have the float needles and seats inspected and or replaced. If the bike ever sat without being ridden for any extended period then you'll also need to have the pilot jets removed and poke a wire (or suitable poking devise) through the opening to remove varnish build up.
It's also possible you could have a vacuum leak, check the rubber boots between the carbs and the engine for cracks.
When was the last time the air filter was serviced or the fuel filter (if fitted) replaced? Have you ever replaced the coils? There are a lot of things it could be and sometimes it could be several things that all add up to a crappy running bike. You'll need to have each issue addressed one at a time to figure it out but when all is sorted it'll run sooo sweet.
good luck,
dc
[ This message was edited by: daytonacharlie on 2007-03-14 07:30 ]