I don't have any advice, nor much knowledge; but can offer only my "two cents" worth, with a side order of "opinion" . . .
I consider the 4.0 as a reliable engine. I have two of those, but have never owned a 3.0. I do see that people who run the 3.0 in general praise its reliability and longevity. And, in my personal opinion, the '94 models were the one of the peak years for these trucks, all the way around, but especially with the drivetrains (bear in mind, that was the final year of OBD1 / EEC-IV).
In all honesty, if I were in your situation I'd try to pick up a second truck, with a 4.0 and manual, as a second truck. As a caveat, of course I don't know how that option fits your personal situation.
Swapping from the 3.0 to a 4.0 would also include the transmission, likely the PCM, and likely wiring harnesses. The right way / easy way, would be to use a donor truck. Anything after the 1994 model year swapped in will increase the complexity of the swap; 1995 went to OBD2. So, your best donor years are 1990 to 1994, with '93 and '94 being the sweet spot.
A donor truck for a swap is the way to go; so why not just get a "donor" that becomes your second truck? By the time you look at the cost and hassle of a swap, just getting a second truck looks more attractive. And if it's a daily, the down time for a swap that may go well or turn into a hassle is a big consideration. In lieu of a whole donor truck, you're buying just parts, which can become a real can of worms . . .
But that's just me. I have a mental defect, that makes me want to collect these trucks.
Like I keep telling my psychiatrist, you can't have too many Rangers . . .