Well, upon some suggestions via PM, I figured a few things out, but not home yet...
When I checked the codes from the onboard LED before I erased them I had codes: 7, 17, and 27.
I read up on the codes here... page 24 reading off pin 3.
http://www.autolib.diakom.ru/CARS2/pribor/cs1000/manual/cs1000_mb.pdf
These codes are Emission related code and the same as reading the codes from Pin 3 of the Diagnostic plug
Code 7=TNA signal(rpm) read by CFI control module
Code 17=Oxygen sensor is shorted to positive or ground
Code 27 =Data exchange between CFI control module and ignition control module interrupted
Now, when I bought the car, the electrical plugs into the EZL were disconnected, so I felt that would explain code 7, and 27, as I never reset them.
I also replaced the O2 sensor with a Bosch Mustang unit, and got the heater cables mixed up, at first, so that would explain the code 17...
Now the plot thickens....
Using my home-made LED code reader, at Arthur Daltons suggestion, I tested pin 14 which is the MAS/CFI pin...
I had a bunch of codes stored!
I recorded then looked up the codes on page 28 of the doc link above...
I had 2,3,4,5,6,7,12,and 13 stored!
I then went thru the codes one by one and cleared them...
What was interesting was each time I cleared a code, there was not a long LED flash as you get clearing the codes from pin 3... ther was no LED flash, but there was a loudish click from somewhere on the firewall behind the battery, and also a stereo click from the front of the engine... I think the smog/air injection pump.
I then restarted the engine and left it idle until it dropped into closed loop...
Then i turned it off and KOEO checked the pin 14 for errors...
Code 3 had reset..
Code 3= TN/TD signal (RPM) interrupted.
I did some searches and found this thread, which details that the 1990 diagnostic is a rarer beast... also Athur Dalton describes a memory clearing reset procedure, which I followed, but the code returned as soon as the car is started!
http://www.peachparts.com/shopforum/tech-help/232393-1990-300te-code-3-pin-14-a.html
Now searching the FSM for a test procedure for the TN/TD sensors....