Hi, I have the same bike and have been working with carb issues for part of the summer. I have made some advances this weekend, I vacuum synced the carbs using the two-bottle method, which works really well if your carbs are way off like mine were - no fluid gets sucked up! Anyway, my Haynes manual says to sync 1&2, 3&4 and then 1+2 & 3+4. The adjusting screws are super sensitive btw.
My exhaust is a Yoshi 4-1-1, and I have been having issues with plugs carbon-fouling. I have it narrowed down to plugs #1 and #4; the inside plugs seem fine. I haven't been meticulous enough to see where on the throttle the fouling occurs, but I suspect it is lower range rather than upper. I have my pilot screws set to 1 turn out each right now, I have experimented as far up as 2 1/2 turns without much real difference. I have gone with a hotter plug on the outside which seemed to make a bit of difference.
The bike runs well except for a stutter in 6th gear between 5500-6000 rpm. After 6000 it pulls hard and fast as far as I want it to go. I am not sure if this is an ignition issue or a carb issue, I am leaning more towards an ignition issue since it is the same coil for plugs 1 & 4 and those are the ones that are fouling. And the problem seems more rpm/engine load related rather than throttle position.
I had a small leak on intake boot #2, so I took them all off and sealed them up around where the band clamp goes, some minor cracks on each. I also found that carb #2 should have a #7 jet needle, the other carbs have a #3. Someone had the #7 in carb 1, whether this makes a huge difference or not I don't know.
Anyway, replaced the boots and the carbs last night, it started up fine and rev'ed smoothly. Took it for a short test down the road, runs about the best i have had it running all summer right now. I will take it out for a longer ride and come back with my findings on the stutter and plug fouling. I want to re-sync the carbs with the freshly sealed boots anyway.
I found a stock exhaust for sale, I am thinking I may need to swap out the 4-1, I suspect too the carb issues I am having are somehow tied into the yoshi setup. All carbs jets are stock, and maybe I need to change the main jet to accommodate the yoshi.
A lot of trouble for a 26 year old bike, but it is my first and I want it to run the best it can. It has under 26K km's and is in good shape overall.
Also thinking about changing my plug boots, removing the 10k ohm stock boots with some 0 ohm boots, haven't made that leap yet.