Issues after having interior torn apart

[Black Ice]

I'm having issues that all started at the same time, the truck is a 2002 F250. I had the entire truck painted so the bodyshop had alot of it apart (hood off, bed off, interior apart, new roof put on, etc...). They had the truck for 3 months in a cold MD winter and now I'm thinking something electrical is messed up. Here are the issues:

1. Trans flashing codes and shifts strange (seems to shift fast through 3rd and holds to 2500 until it goes into OD).

2. Fuel Pressure Gauge reading strange - Autometer electric in cab guage. It started reading well over 100psi, normal around 62psi and today 35psi. Only changes when I turn truck off and back on again. I just put a new filter in it the other day as the fuel in the truck was 3 months old.

3. Won't start under 50 degrees without being plugged in for 30 min or so. Once warm no problem. In the 50 degree range when it starts smokes and real choppy for a few minutes. I have replaced the GPR before and had no issues before it went in the shop.

I am the original owner and have 196k on the truck. All these issues have started around the same time so it's leading me to believe it's electrical since the truck was all apart. The batteries (both, not replacing 1 at a time, big no no!) were replaced in Oct. 2010... Help! lol