Not having the extension piece only means that the bolt in the engine harness 60 pin connector would not retain the harness as intended by the factory which you alluded to in Post #8. Not ideal by any means but like the General stated and you have done punt it until you resolve the issue to rule it out.
In all honesty I would say it probably does little more than a good tune up and bumping the timing to 14 degrees did back in the day if the motor is stock. I am one of those guys that fully believes that the only way you get your money's worth from a tune it to put it on a dyno and tune it on a dyno. And if you are doing this you better have changed the heads, cam, intakes, injectors, cold air intake, etc otherwise tuning a basically stock EEC-IV motor won't net you the hp to make the dollars spent worth it unless you are in some type of stock class racing bracket or series.