The temp gauge will go to full hot when the engine kill switch is set to "off", that's completely normal.
If there was an engine swap, make sure the ECU and the sensors are correct. For example, the early Busas used a 16 bit ECU and a different sensor to run it. Later bikes (I think '02 and up) used a 32 bit ECU and had a different crank pickup. Make sure all the sensors are plugged in the correct places, there is at least one connector that can be plugged into the wrong sensor, I can't remember which 2 use the same connectors at the moment....
I'd also post this in the "All Motor" section, there are some very sharp people in that area who may be able to shed some light on your issue(s)