6TS 3406E electrical problems

I bought a 2001 peterbilt, 18 sp, 3406E(6TS) from a guy a couple weeks ago, here's what he told me about it - he bought the truck to re-do it and sell it. Had a big cam cummins in it with a spun bearing, so he pulled it out and put in a 3406E that he had. Truck runs great, really strong. It has some electrical problems though, Jake brake won't turn off(have to keep my foot on the clutch if I want it off), cruise control won't work unless Jake brake switch is on, water temp gauge doesn't work so in turn engine fan won't kick on when it's supposed to. Anyways, had a mechanic come look at it and he said to take it to a cat dealer and have them re flash the ecm to stock but to leave the hp rating of 600hp or ask them to up it to 650hp. Will this work or will the cat dealer put a low nox tune in it and then it will run like crap? The guy I bought it from also told me it had stock c16 turbo, cam, and injectors. Pulled a 100k lb gross load the other day and it pulled great, just have the minor electrical problems. The mechanic that told me to get the ecm re flashed told me this will solve a lot of my problems. Opinions?

 

Also the mechanic plugged into his cat ET and couldn't change anything so that is why he recommended the reflash

 

Amarillo Texas

 

The 3406 in my truck came out of a 1991 kw w9