[Notrodder]

Sure, you could do it, but you'd be better off, in the long run, if you keep looking around for the truck that you want in the first place. They are around, and may be lower in price due to the popularity of automatics these days. Probably the best that you can do for yourself would be to develop an idea of the perfect truck package for you, then look for the truck that is closest to that package. Any compromise (and there will be compromise) from that package should be subtracted from the price you are willing to pay. That way the money that you would have spent on changing components can be spent on repairs (and there will be repairs).

About your transmission choices:

A truck with a clutch is far better than an automatic in difficult situations, like mud, or a tough hillclimb where being in the right gear at all times is important.

A good driver with a clutch and shifter is an active system that can anticipate what comes next. An automatic transmission is a reactive system with a slight lag between now and when it shifts to the gear it needs (except for manual downshifts), which is fine for the street, but less than ideal for 'off the pavement' operation.

I've had trucks with automatic, three on the tree, and four on the floor. I, by far, prefer the floor shifter with a clutch. The drawbacks of the automatic make it less than ideal for my uses in a truck and the column shifters linkage (sewing machine parts) is problematic.