If you plan to keep the Runner, I would pull the block and rebuild it. I would bore the block and consider some head work. This along with the headers, a moderately open exhaust, and a better intake should give you good results. If you do the work yourself it should come in under $2k, about $1500-2k cheaper than doing an engine swap.

This is assuming you have a 5-spd and not an auto. If you have an auto tranny, I would sell the Runner for what you can get and buy a 3rd gen w/the 3.4. You can find them starting at around $4-5k

More than tread lightly. Leave it like you were never there, nor anyone else.
'90 X-cab 4.88's 33 BFG AT's, rr ARB, Headers, Ignition upgrade, cold air induction.
'91 X-cab 5.29's 315's BFG MT's, rr ARB, custom bumper and flatbed