2005 5.9 with 143,000 miles causing SO MUCH TROUBLE
 

So here's a little background on this truck:
I bought it from a mom and pop dealership with a 1 year warranty. 3 days after the purchase, I start noticing electrical issues (extremely dim headlights, cab lights coming on and off, needs jump to start). Obviously the first assumption was a shot alternator which is covered by the warranty. We take it to the shop and try TWO brand new alternators and neither of them take which points to more serious electrical issues.

Diesel mechanic says it needs a new wiring harness (NOT covered by warranty - we demand the dealership to pay half since it is less than a week after the purchase). We get the truck back (after about 2 weeks - slowest mechanic ever) and it drives fine for a couple of days.

I have a diesel mechanic at work check it over just to make sure it's good to go - he checks EVERYTHING including the injectors which he says are firing beautifully. No codes were popping up on the ECM.

We take our pretty new truck for a family dinner with my 4 year old in the truck and BAM the truck dies at 60 MPH and we get rear ended and completely total this poor foreigners pontiac. He doesn't have insurance and speeds off before the cops show up.

The truck would no longer start, gauges were not reading what-so-ever. Everyone concludes the ECM must be shot so we take it to get rebuilt (there goes another $700). We pop the ECM back in a week later and it starts up BEAUTIFULLY. Let it run to warm up and it kills itself but starts right back up afterwards - we notice some smoke coming from somewhere (it was too windy to tell from where).

We scan the ECM and get the following codes: 1652, 2509, 336. We clear the ECM, drive it around the block, and scan it again and only get two codes: 541 & 521. Truck wants to run rough, idle rough, and now there is a KNOCKING in the engine that was never there before.

We are completely stumped at this point. Could the ECM have been flashed wrong? Is this something more serious? Is it possible that the original wiring harness "fix" wasn't fixed correctly?

Any suggestions are appreciated! Sorry for the LONG story.

First did you clean all the grounds on the batteries? Check the grounds on the block?
A bad ground will do everything that you stated including shutting the truck down!

I want to say yes but at the same time I'm unsure of where every single ground in the truck may be. Can I find a diagram online somewhere?

No just trace the grounds from the batteries that will be enough.