If you remove the electrical wires for the EHA and IACV then the car will run on without sensors. This puts the car into 'K' Mode and not 'KE' mode. The O2 sensor throttle position switch and temp sensors will not have an effect.
If the car still misfires in this condition then it wont be the ECU commands that are causing it.
If there is no electronic control of the injection and you are still getting the misfires it will be elsewhere.
Have you had the fuel pressure check done? If so what was the result.
Did your Indy Bob put another set of leads on to check? Even new ones are known to have some quality issues.