Changing the exhaust is not necessarily an "upgrade" AND you should not be making ANY mods unless and until you solve your present problem.......or decide that it's "normal" for that model.I want to upgrade the exhaust and get it jetted, hope that would fix the carb issues.
I'm still checking the forums, just wondering if anyone knows. Maybe the bike us just cold blooded.
What about the air filter? Stock or something like a K&N ??
If it's not stock, you might be AMAZED at how much better it runs if you put a stock one back on it......like not needing any choke when hot.
A double dose of Berrymans B12 Chemtool wouldn't hurt and might get something that the manual cleaning missed. Also "tweeking" the idle mixture adjustment screws out a turn or so might help a lot.
If the valves are adjustable and you don't KNOW if they were ever checked, NOW would be a good time to do that. Ditto for the plugs.