Jumpers on the board to be programmed do not affect the 13.5v voltage.They just affect pins 12 13 (if i remember correctly) which are the data anche clock pins for programming.You must have shorted something if you don't get the 13.5v and the transistor is that hot...

So the problem is deffinatly to do with the COMIII, well the COMIIIis a mess, and i may just re-do it.