Assuming the 4runner had a 3.4 swapped for a 3.4 and not a different motor all together, its a nut and bolt job. Nothing to worry about other than the condition of the new motor. If I wanted to buy the vehicle Id probably ask to do a comp test. If it checks out, you are taking no more of a gamble than buying any other used engine/vehicle
This doesn't make sense to me "I'd throw out an offer of $5000 considering there will likely be little to no resale value." I think you just proved it has resale value, possibly $5000 resale value
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Good luck with your hunt.