Failing that, it could be electrical,
My twinshock ran like a pig when hot, fine cold.
Traced it to a faulty stator coil. Check yours against the data in
www.srx600.net ?
Prolly not this, I've never heard of anyone else having this bother, but you never know. It drove me nuts for weeks!
Try changing the plug too. Another funny one I had was rough running traced to a spark plug "unwinding" and the electrode disappearing up the thread. You can imagine that it doesn't do combustion any favours!
Next, make sure the tappets aren't closing up? Maybe the locknut could have worked loose from the service?
And run it on "prime"; this just bypasses the silly fuel tap. (not sure about mono's tho)
good luck!
andy