Personally, I'd go with the 5 speed manual swap.
Use a T-5 trans and a cable operated clutch. Skip right over the M5OD and its problematic hydro clutch. It'll be a little more work to install a T-5, but you'll definitely save yourself from getting headaches later.
Or rebuild your auto with high end aftermarket parts, like B&M clutch/band kits and such. (if they offer the parts for your transmission)
Either way should be about the same in terms of cost. Figure around 1500, doing it yourself with the manual swap... or having the auto rebuilt by a pro, but removed and installed by yourself.
Prices may be higher or lower where you are, since I'm basing them on what I know about the costs in Michigan.
1996 Ranger 3.0, 5 speed stick, 4x4, 3.73's, 31" BFG AT KO's
Wiring, it's all fun and games until you poke yer eye out with a soldering iron...