Well, despite all the documentation that the ECU is rarely the issue when it comes to running problems I have determined that the ECU is the root of all my issues. Let me explain...
This all started yesterday morning on the way to work. I was driving along and all of a sudden the RPM's started dropping and the engine began to run like shit! It was stumbling and sputtering, but I was able to get it to the parking lot at work. I checked all the injectors by pulling the plugs and listening to the engines response to determine if that injector was firing. I found that cylinder #1 and cylinder #3 injectors were not contributing at all. I then flipped the harness connections on each side and the motor ran the same with the issue following the harness. I then went about checking the ground connections and other sensor connections but it made no difference. That was about all I could do while sitting in the parking lot so I took the drive of shame back home on two cylinders with my hazards flashing the whole way there.
Over lunch I pulled the distributor and checked the trigger points but could not find any issues. I also check the harness really quickly with a ohm meter and everything checked out fine. However, the car still ran on two cylinders.
Last night I decided that I needed to pull the entire injector harness from the car and check each wire individually. After struggling with rust bolts, I got the brain and harness out and on to the work bench. I tested every wire to and from the brain, no issues. I then decided to reinstall the brain with another harness I got off a dummy motor (1.7L dummy motors are not hard to find). That harness also checked out find and looked a little better than the one that I had. After getting all that wired up the issue was still there no matter what I did.
Finally, I went about changing the brain out with the one I got from the dummy engine. It is interesting to note that the ECU installed in my car had a "Remanufactured By Robert Bosch Corp" sticker on it. After hooking up the new brain, the car started up and ran PERFECTLY! I could not believe it. All the documentation says that the ECU rarely fails and when it does it is usually completely dead.
After reviewing the ECU wiring diagrams, you can clearly see that the injectors that go to cylinders #1 and #3 run on one driver while the other two run on the other. It appears that just one half of my ECU failed on me. When I get some free time I will open it up and determine if the failure is something obvious. I am just glad that the car is running again as it is my daily driver.
-Britain