Problem No. 1
Due to the engine
configuration and the extremely tight packaging the temperatures in and around the engine are high. Even when riding with proper clothing your right leg gets toasty. With the engine
solidly mounted to the frame the frame gets very hot.
The heat is really apparent during street riding. The best way to cool it down
is not to shut it off and wait, but to get the speed up above 45 to 50 mph so
the radiators can do their thing. The upper radiator has two fans on it but the
switch contacts much too late, about at the point where your leg starts smoldering. You could easily wire the fan's power supply in parallel through a switch
to take some control of that.
Suggested Solution: Big radiators. Other things help like improving the fans and their set point and running water (with wetting and corrosion inhibiting agents). This is not a cheap or easy fix. HRC upper rads do not have a tap for the thermostat bleed and have a connection for a bulb type temp gauge that you may or may not need. I like electric gauges myself. HRC rads also do not have brackets for fans, you'll have to add them yourself.
Wrapping the exhaust headers in ceramic heat resistant tape also helps. I did this on my project bike and it is a noticeable improvement.