"Look for the ECM- if it shows
"Look for the ECM- if it shows Delphi on it and is about 1-1/2" x 4" x 6" with a large connector on each end, it's probably a MEFI 1 controller and AFAIK, this wasn't actually self-calibrating and was a very simple program. Was the rep in the service department or sales? I would call and ask for technical help and you may get a different answer. I worked on MasterCraft boats and Mercruiser when I was in the business and both originally used the Delphi controller. In '98, when I was at the Regal dealer meeting, I talked to the VP of service for V-P and at that time, they were still using Delphi, so I think the systems were pretty similar between MC and V-P, although Merc had changed to a Motorola controller.
Look at the front corner of the throttle body near the throttle plate for a four-wire harness that has a pair of blue wires and a pair of green wires. This is the IAC (Idle Air Controller) and controls the idle speed, via input from the ECM. Each wire has a white or black tracer on it but unless they were yanked out or damaged, it's not going to change and for this, their positions don't matter (if they're in the wrong position, the IAC won't work properly).
Why was the motor rebuilt? Has any electrical work been done on the motor?
The things I would check now are:
All ground connections for the ECM, main harness, knock sensor module, distributor, relays, block and the battery posts/cable clamps. If you have the GM distributor with two harnesses on one side, make sure the IC module boats aren't corroded and are snug. If the cap and rotor are old, replace them- same for the plug and coil wires. Look on the coil for cracks and carbon traces. Old plugs? Get new ones. Check the base timing- this can't be done without putting the ECM in diagnostic mode. Some scan tools have a button for this. If not, you can use a paper clip- let me know if you do or don't have a scan tool with this feature. The idle needs to be at 1000RPM to set the base timing to 10º BTDC. Any time a motor is rebuilt, this needs to be set and just putting the distributor in, getting it to start and calling it good is not going to work."