It's not the computer. The circuits that are acting up are not computer-controlled.
It sounds like an issue with your fuse links, which are the small loops of wire plugged into the harness near the positive battery terminal. Fuse links are basically slow-blow fuses, and shouldn't pop on their own--hopefully if they are bad, it's due to corrosion or mechanical damage. If a link is fried or broken, or its plug is corroded, or the guy didn't reconnect the fuse links properly when he replaced stuff (sounds like he replaced the terminal?), that'll be why it's missing power to places. Could be the guy screwed up; could be something was corroded and didn't give you trouble until he flexed the harness to get the terminal off the battery. But, yeah, check that your fuse links are intact, and if the terminal was replaced, make sure the fuse links are still connected to it.
You may also have an in-line blade fuse holder hanging off the + terminal if your truck has/had the factory fog lights. This is unrelated.
The wiring diagrams in the EL section of the manual may help you narrow down which fuse link(s) aren't working right if you can't find the problem visually.
Not sure about the trans hesitation. Is the fluid level correct? Might not even be the trans. Mine had an engine stumble just off idle for a while, and IIRC it was that damn MAF plug.