6.5 turbo diesel rough idle

I have a 94' GMC K2500 with the 6.5 diesel and it has been running rough at idle. It will idle at 1000 rpms and every few seconds will puff out a little cloud of black smoke. I have an OBD-I scanner and it has codes about the transmission slipping and a short to the PCM5. I have a towing chip in the computer from Heath Diesel and has been doing well pulling a stock trailer but now has this idle problem as well as the service engine soon light on. Also sometimes when the light is on it won't shift into overdrive or lock up the torque converter. Any ideas what might be the problem?

With the SES light on the computer will not allow a 4th gear or lockup....This is normal ..

My first suspect is a failing PMD

Is the PMD remote mounted ???? And when was it last changed.....These are a failure prone part.....

Stalling at idle is a classic indicator of PMD failure

Keep us in the loop....

My PMD was relocated to the firewall to the left of the brake booster a couple of years ago.

I would replace the PMD
Is the PMD on a heat sink ???

Best place for the PMD is down in the bumper just slightly away from the nostril to keep heavy water splash off of it....

Anywhere under the hood gets hot....With summer heat in the 90-100 + F range the underhood temp is smokin hot

Make sure to apply heat sink paste to the PMD contact surface and snug the screws down.

The surface needs to be flat to stop any flexing of the PMD.....

Let us know.

Any stalling issues with these rigs always points at the PMD as a suspect.

A scan tool will rarely diagnose a bad PMD.....But can lead you on a crazy wild goose chase.

I am not saying that you do not have other issues....Get FRESH PMD on thew rig, clear the codes (Unhook battery for a few minutes) Give it A GO....

https://g.co/kgs/UWWF3zh
This what I used to relocate the PMD

THAT WORKS.
Get a fresh PMD on and see if the issue resolves.

Get the cooler out of the engine bay and in fresh air.....
Underhood temps can get very very hot ...The micro electronic does not like HEAT

OK I put a new PMD on the truck and that didn't fix the problem. I have an OBDI scanner and the codes that are listed are: DTC 38(brake off), DTC52 (System voltage High-Long test), DTC 57 (Powertrain control module 5 volt shorted), DTC 68 (Transmission Component Slipping), DTC 24 (Transmission Output Speed Low). I have tried to clear the codes but it doesn't seem to work. I have tried unhooking the negative terminals on both batteries and tried to clear them using the scanner as well but to nothing seems to be working. Any ideas???