If you don't have a body lift on the truck, it will be easier to pull/install the tranny and engine as a unit. You can pull them seperately, but there isn't a lot of room between the tranny and cab to loosen/tighten the bell housing to engine bolts, and it is harder to align the engine and tranny inside the vehicle.

How many miles are on the 4-Runner? If they are high, it might be better in the long run to just rebuild the 3.0 from the truck.

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