RE: I feel the need...
You're better off swapping in a different transmission. If you're planning on running tires larger than 35s, I'd also plan on swapping transfer cases and axles. The rear axle needs to be swapped anyway, but the tcase and front can hold together a little longer. That's with a mild 350. If you plan on swapping in a built engine.....you might as well just go ahead and swap everything out at once if you intend to beat on it.
Advance Adapters, Novak, or Rube adapters can help you bolt it up to the factory Tcase if you wish. AA, Novak, and many others can provide you with the mounts to install the engine in your Jeep if you aren't planning on making those. Then you have to address the wiring, cooling, and fuel system to make it work.
There's exhaust, plumbing, and accessories that you have to deal with.......
It's been done so many times that it's hard to call it difficult, but it's not a cheap drop-in deal like people make it out to be......not if you do it right.
How much power are you shooting for? Do you have a 4 or 6 cylinder? The 258(6) can be built to produce some respectable power levels.
edit: I just reread your post and realized you don't have an 88 model, it's the 94. Okay, if you have the AX-15 5 speed then you could use that with a really mild 350. Also, if you have a 6 cylinder, it's a HO 4.0 not a 258 like I typed earlier. I wouldn't waste my time swapping in a mild 350 if you have a 4.0, just build it.