ODB1 Tuning questions

I have been replacing parts chasing an intermittent cutout in my 88 gmc dually. Im basically to the ecm and swapped a reman from autozone and put my chips in. Its acts like a 3 speed instead of a 4 speed and know this is a pretty basic question but any ideas on where to start getting a new ecm just to confirm this one has a injector defect or suggestions on what I can buy that would improve this computer? 1988 GMC 7.4l TBI Crew Cab Gas Guzzler...

Computer that came out of it says reman 2015 OE replacement 1227747

replaced parts include

alternator, rebuilt tbi, fuel pumps, fuel pump relay, fuel pump actuator (dual tank), ingition coil, distributor cap/rotar, wire, plugs, maf, clean and polish grounds.

Symptoms after long term driving will get a stall at low speed and will start up once pulled over and stopped. With new ecm and my chips physically moved over it starts easier and seems to have more power. Waiting on a fuel pressure guage tool and odb1 tool in mail as first steps.

ordered a SST27SF512 Flash Chip and eprom adapter for the 2nd computer and will start with reading the chips and trying to see what is different and make a copy of my original setup is end goal. I guess my main open question is what doesnt "plug and play" when you buy a new ecm with same OE# and move your chips over if someone with experience on the topic can help.

you have replaced everything except the harness right
all 35 year old wiring is suspect

That is a fair assumption harness tests ok and I traced my fuel pump relay with a tone and probe tool, I used some dielectric grease and reseated it a few times and the cut out is not consistent so being suspect of harness is fair but the truck is low miles southern california truck and have more rust on my new prius lucky for me :). Right now its running with the old computer in place as I did not put over 10 miles on the other one, I did about 50 slow speed shift cycles through the neighborhood and had the same result. Is there a break in period, or anything that should impact my shift at 45mph between old computer with old chips, and the new replacement from local parts store with my old chips? On my side I'm less concerned about solving the cut out on this thread and more about understanding why does the computer behave so differently with the limited knowledge I have of TBI and what direction should I go to create an exact copy of what is in my truck today with the old computer.

the computer with the same chip should behave exactly the same after a power cycle (clearing any ram stored learning data) as it is running the same program. if it does behave differently there must be a fault in one of the inputs or outputs