Well, I found the problem. There is a burnt trace on the ECU circuit board leading to pin #46 (sig rtn). This explains why all the sensors on the sig rtn circuit were reading out of range and why the engine was running so badly. The cause of the problem, however, was a bit more difficult to find.
I didn't know at the time but, when I bought the harnesses I was incorrectly supplied with an O2 sensor harness for an automatic transmission car instead of manual transmission. Automatic cars supply 12volts through the neutral switch circuit where as manual transmission cars work with the 5volt vref. The cross-over is done in the O2 harness. The first time I stepped on the clutch it dumped 12 volts down the sig rtn wire and cooked the computer.
The fix was simple...just move one wire in the O2 sensor harness plug. Unfortunately, now I need a new computer. Anyone have one for sale?
Anyone planning an automatic to 5spd tranny-swop should make sure that they get a new O2 sensor harness if they are planning to change to a 5spd computer.
Thanks again for all the help! With any luck I should have this thing back-up and running sometime soon.