Wow... this sounds very similar to the issues GM had with the FSD on the 6. 5 diesel, except they were smart enough to make the electronics a totally sealed unit that could easily be mounted any where you could get the wires to reach.
My VP is pretty much toast, truck still starts normal, but runs really odd, kinda like the timing is stuck at one spot, blows a lot of black smoke(well,more then normal), and has very odd throttle response. Truck has 60k miles on it, has had a TST PM3 comp for the last 20K, and an EZ stacked for the last 6K or so.
Would be real nice just to replace the electronics and remote mount them some where with less heat.