I have jelibuilt tunes, but havent put my exhaust on yet, my transmission has a shift kit, but not sure how built it is beyond that. It had just been rebuilt right before i bought the truck, so i dont know the details. Once I get the exhaust on, then I can play with finding the right tunes for my driving.
The cost of the manual swap isnt that crazy. For whatever reason you can get a zf5 with like a stage 2 clutch for significantly cheaper than you can get a good built e4OD. Its also not my daily driver so if its down for a bit, not a huge deal, however I dont know if I trust myself to do the work, so the labor probably evens that out or makes it slightly more by the time I round up the needed misc parts.
I know more power will help, but I get concerned about reliability at that point. This is my road tripping truck. Dont want it to give out 1000's of miles from home or deep into baja. I think exhast and intercooler would be as far as I'd go to engine upgrades.