Try a PCIII and a map to suit the full exhaust.
RCs don't like low rpm the way it is, let alone a map that doesn't fuel/air mix the bike properly.
These are hot engines....they will run hot even if tuned correctly, just the nature of the beast.
I remedied this some what by using engine ice.
I agree. Get a power commander and have it dyno'd to create a proper air/fuel map for the engine.
Simply put, if you want a bike that putts at 2000 RPM, get a Harley.
These bikes do not like to be lugged below 3500 RPM. They show their displeasure exactly like your description.
Just one RC51 throttle body is bigger than what feeds both cylinders of a Harley, and you have two of them.
It's actually more of a complement it runs as well it does at those low RPMs.
Keep it around 4000 RPM and you should have no problem.
My bike in stop and go traffic can get up to 221 deg F.
My fans start at 218 and cool it down to 205, but it cycles up and down until I can get into moving traffic.
The critical temperature is 251 deg F where the temp indicator starts blinking on the instrument panel. Pull it over and cool it down, or kill the engine.