So basically what we have learned is that Turbo 3B = bad. I"m guessing a tired 3B is just a few PSI away from crank failure/spun bearing. Despite what people on mud do, the 3B's usually aren't long for the world when turbo'd. How old is the newest 3B? (not 3BII) 30 plus years? I think it's too much stress to turbo those.
The 3B wasn't made for US highways, and in a big heavy troopy it's even worse.
I think this is a good time to decide exactly what you want to do and can do with the troopy. Aside from finding a "cheap" 13BT, 14B, 15B you are looking at a full swap. Realistically, most of these will probably need a rebuild or a chunk of maintenance done.
LS is the "cheap" swap and lets you fly down the highway with OK mileage and unlimited parts supply. No where near as cool as a diesel, but actually getting out and driving and exploring is much cooler than a project in the garage.
I'd say 2UZ, but that swap is more involved than an LS.
I don't like the 2F/3F/1FZ swap as they are just as complicated an LS and then you are still slow and old tech unless you rebuild to Mosley motors spec and thats not cheap.
I would love to see you keep it Toyota, but I understand you have a budget/time constraints. A full 2UZ Cruiser/tundra setup in a troopy would be pretty damn sweet. 2UZ are usually pretty cheap.
It sucks it

out on you.