UPDATE: Diagnostic Dynamite
Struck diagnostic gold again...
After many diagnostic hours using this GOLDEN resource it was determined that our replacement ECM was shot. This was a good replacement ECM so we never thought to look at it until the end of the diagnostic period. In order to make a long story short, the problem was due to LATE MODEL RESTORATION part LRS-8793XSHM (1987-93 FORD MUSTANG O2 SENSOR HARNESS, MANUAL TRANSMISSION - FOX BODY).
One of the "Benefits" of the part is supposed to be "Plug & Play Install." In reality, its more like Plug & Pay More Install because this product WILL fry your ECM. Our harness came jumpered for an automatic. Therefore, as soon as we plugged it in and turned the ignition key it fried the ECM. Yes, the car still ran, but it was sluggish and had several trouble codes that led us on a wild goose chase. Eventually our tech traced the trouble back to pin #48 and a 3mm long burn inside the ECM. That's stinkin A+ diagnostic work!
Once the tech found the burned out pin #48 he researched possible causes with the manual above and the good old internet. While on the net, thank the Lord, he found a pdf about another guy having the same problem (wrong O2 harness). After reviewing the pdf he was able to make the needed repairs and I got to buy ANOTHER ECM. Thanks Late Model Restoration (sarcasm)! Do you know how hard it is to find an A9L processor these day? They are expensive now too. Thanks again Late Model Restoration (sarcasm). I wonder if they will foot the bill for a new ECM since there product was not "Plug & Play," as advertised?
In the interest of helping others, below is the attached article (pdf) on the problem and how to avoid it.
Since the resolution I have put about 150 miles on the car (300 since rebuild). It has an erratic idle at the moment so we are going to perform a base idle reset with TPS re-adjust and go from there. It is also believed that there may be a slight vacuum leak due to a high pitched whistle from the engine bay as well as no cruise control (all elec checks out fine in cruise circuit). Updates and more pics on the way...