Hmmmmm.....that's an odd one.
None of that makes sense with just an OPS change.
The OPS powers the lift pump (except while key is in "start" position, unique to 95 models only) as well as drives the gauge on a 95 , but it doesn't keep the engine running after a "key off" event.
I'm going to guess it's actually an ignition switch problem.
here's a pic that will make the rest of this post a little "clearer":
You might think that and OPS keeping the lift pump running might keep the engine running if it fails on shutdown.
But, the key shuts off the the Fuel shutoff solenoid and the PCM shuts down the PMD, which no longer drives the fuel solenoid once power is removed from the PCM (IE: key off). The fuel solenoid is what determines the injector pulse to the cylinders. Stop driving the fuel solenoid and there's no fuel delivered to the cylinders.
Remove power from the PCM/fuel shut off solenoid and the engine will stop. No questions asked as the FSOS is powered open. Remove the power and the FSOS slams shut, cutting off fuel to the IP.
Somehow, you're still getting power to the PCM/FSOS which leads me to say "ignition switch". That seems to be the only common point of failure in the systems you're having troubles with.
The ignition switch is very "glitchy" on GMT400's when they get old and worn. I'm going to guess your OPS change/no shutdown problem is a coincidence.
Now, if someone has messed with the wiring, all bets are off...something very "weird" could be going on and power going where it's not supposed to.
Keep in mind; without actually seeing and troubleshooting the truck, I'm guessing here....