What is the battery voltage with the car off? When the car is running at idle? and then with the wipers, headlights, and blower on. If it is not 13.5 or above under all those vconditions you are gonig to have problems.

Honestly it sounds like you have charging, battery, alternator problems that are completly unrelated to the EFI. If they were so bad that you had to replace the harness you have major problems that need to be addressed. It will never run until you sort out your electrical problems. Im surprised that any reputable shop would take your money to install the EZ EFI if the charging system problem was that bad.