Air in the system isn't the only thing that causes low heat. A broken thermostat that is stuck in the open position will cut the heat considerably - I had this problem which made riding with the top down on cool nights not fun ! If nothing has been done with the cooling system that would introduce air, most likely its the thermostat.
Ok so the temp sensor wires can't be crossed - just a wild idea but at times our fuel gauges will stop working for no good reason and you just disconnect the battery for a few hours and presto the fuel gauge works. Maybe the temp gauge is the same ???