What are you mods? Intake/Exhaust?
I have an '05 and was having idling issues, rough running and hesitation/lag at higher speeds.
It was a combination of all these things to get it back to 98% perfect.
1. Front two plugs were fouled - Cyl #1 was running too rich. Cleaned. (old plugs had fouled last October so it was going downhill since after RAA-West)
2. Cleaned and oiled entire throttle control area and cable. Gunked up bad. Helped but didn't fix.
3. Bad gas in Florida. Ran lots of STP water treatment and Seafoam through it but ended up draining tank and putting in a new fuel filter. Helped a lot as old filter had 60K on it (oops, don't wait that long).
4. Checked Primary TPS (OK) but found Front TB was off. Rebalanced it and it helped. Needs to be done again after all the other work.
5. Battery - couldn't keep bolts tight. New battery helped.
6. Installed a different map: Power-Tripp-Jardine 3xK&NRU-2780a, reset adaptations, 12-minute tune. Helped a little.
7. Discovered that the crankcase filter was horribly clogged. Cleaned it and will check and replace it when I get home.
-- I'm hoping it was due to the poor running condition and not a more serious internal issue.
8. Kickstand delete wire splice went bad. Redid splice, ordered used sensor connector and installed. Seemed to help. Check for electrical shorts, our ECU is finicky!!
9. Crimped and added dielectric grease to all 6 coil connectors again.
10. My bike runs best on Sunoco 91 Octane but it's hard to find 91 here in FL. 93 makes it idle high and 89 seems to run weak so I've been trying to add fuel every 100 miles and alternate top-offs with 89 & 93 if 91 isn't available. May not matter as much after all the fixes.
11. Main MAP hose was loose and even came off causing bad hesitation at speeds over 65. Replaced all 4 hoses plus connector. Zip tied the ones on the connector.
THAT last step did it - it is Much smoother at idle and has zero hesitation at all speeds now and runs strong. Almost like new!
I removed my stepper motor years ago and set idle manually but others will need to consider checking ISCV.
I removed the butterflies a long time ago but others will need to check Secondary TPS voltage along with Primary and ISCV.
I also ordered additional positive & negative terminal cables to double up and a used coil with two plug wires but didn't install them yet. Swap coils around if you suspect one is bad.
I'll keep the entire list for others but you can ignore the ones you've addressed already.