And the answer is: rich. Cold = needs more fuel to run good. Hot = needs less fuel to run good. You need to lean it a little when it's hot out.
Pull the carbs. Check the float levels, set them 1/2 mm lower (leaner) than stock. I remember the setting is 3.0mm from gasket surface, so set them to 3.5mm. If they are warped, one is lower that the other, then do the best you can.
Buy and install the remote fuel screws. This allows you to set the idle-1/4 throttle mix as the conditions change. All bikes are different, some like 1.0 turns, some like 3.0 turns. These are an awesome addition.
With the open exhaust, you only need to increase the mains slightly, go up one step only. But, this is not needed if it's really hot and humid.
Set the throttle sensor to the correct voltage at closed throttle. I don't remember the value (0.6v?) If this is off, it can create that big flat spot at 3500 rpm.
Are the valves in spec? It will effect the mix also. Tight = leaner, loose = richer. It's a very small change unless the valves get very tight.
Good luck. dz
"Dad, can I get a motorcycle when I grow up?"
"Son, you can't do both"