if the new ecu matches the old one exactly(90/91-94,awd/fwd, 5spd/auto, turbo/non) it won't be off at all. The SAFC doesn't mess with the ecu itself, it messes with the signal from the cars sensors before they get to the ecu.
A TOTALLY dead battery will reset the ECU, not the SAFC. The SAFC has its own battery.
Old gas and a reset ECU will make the car run poorly a bit at first. You need to drive it a bit, normally, in traffic etc, to allow the ECU to relearn its various trims.
Depending on how long the car has been sitting, I suggest you do a few more items on the car tho, really check it over and change a few fluids, plugs etc.
Set the SAFC to 0 on both lo and hi, unless you have a different maf, injectors, pump or fuel pressure. Then leave it alone.
Once the car has been driven for a week or so, you can play with the SAFC, but you NEED to do some homework in that time.
And you NEED to get a datalogger. Dataloggers are cheap, cheap. And there are sites that explain how to tune with the SAFC. There is a section in BCDSM forums that is called "preexisting support" that has several links to tuning pages. Also google it up
Good luck.