[Overdriven]

You mention finding it hard to find gears. Floor shifters have detents for each position and from a cursory search so do column shifters. What if anything the previous did to modify the detents on the column and adjust the linkage is likely your problem there. If the truck has floor shift the linkage might not be adjusted properly or they could've installed the wrong detent in an aftermarket shifter.

I'd figure out what the rear gears are before deciding on a transmission. You may not need overdrive with your gears and can go the more budget friendly route with a th400. If you do go overdrive I'd go with a 4l80e. They're fairly inexpensive from wrecking yards, just need the controller and that's not too bad as there's a couple sources. You can shift the 4l80e manually from the shifter, the controller is there because there's solenoids in there that need direction whether shifting manual or auto.