if the cpu is shorting the finals into TX mode and you do not have it hooked to a antenna is a good chance it is getting hot due to no antenna hooked to it.
with your lack of radio test equipment every time you hook it up you could be making things worse. you sure need a dummy load to hook the radio too so you are not burning the finals up if it is TXing.
anything is possible at this time. so be careful with the radio.
Are these two little boogers the ones you are referring to? I touched the Burt looking one with my finger and it was smoking hot. Could this be my problem?