For a 1st gen truck, personally I would use the 3rz simply due to size.
Toyota was hit or miss as to whether the crank was drilled for the pilot bearing on vehicles with automatics so it is a good idea to get all your parts from a donor with a manual trans, preferably the same donor. My donor was a rollover with 103k on the clock and the entire truck was delivered to my house for 1400.
I would have to check years but for a 5vz swap, I would avoid the later 5vz engines with a throttle motor, although that is personal preference.
On my 87 4runner I used a 1998 3rz from a wrecked 2wd 4runner which has the 2 coil packs, I would have rather used a 2000+ with coil on plug setup but either will work, the only one I would refuse to touch is the early version with the distributor just due to parts availability.
Now looking back (almost 3000 miles later), if I had to do it again I would have probably used the 5vz instead for the simple reason that it was made to fit around the IFS front end and a hole in the hood looks kinda 8). Overall I have been happy with the 2.7, bolted up to the existing trans and transfer, it has plenty of power even with the heavy ass 255/75r17 guard dogs on 17inch FJ steelies, factory 4.10s at 7000 feet elevation. In the near future I will be re gearing to 4.88s more to limit the top end, there is no justifiable reason for a 87 4runner to do 120mph
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