I have had the pleasure of blowing at least 1 ECU in the past month. Maybe 2. I have tried a bunch of different things, and have finally found the problem.
After a year of solid driving, my wiring harness has actually corroded enough so that one of the wires has broken.
If you are having problems with the same sort of thing, I would suggest looking at the wiring harness specifically in the area where the KA harness is mated to the SR harness.
You can get the correct wiring setup instructions from Heavy Throttle in their FAQ section.
In my case (no spark, no fuel, but still cranks) it is the ECU Relay wire (red with black stripe) that was broken.
I am still in the process of checking out the rest of the harness but this is what I have so far.