Normally I'd say go get a spare but you have a 97 with the larger turbine-style MAF and they cost $100's the last time I looked. Even used ones run about $50+. The testing procedure for the MAF in the factory service manual is sort of complicated so a single reading may not give a true picture of what's going on. However, one of the wires on the connector should be providing voltage with key on (I think it's the bronze colored pin) with the MAF disconnected.

Any voltage or resistance that is out of spec WILL throw a code though so if no codes, MAF is fine.

Would it make sense that a MAF would just fail? I mean it was working before the engine change correct?

That seems like a good lead, but I don't know.

All I have to contribute at this point is a dumb question: Was the new engine running before you swapped it in?

No, it's not. Because of the waste-spark system, off by 180 degrees is actually in time. The sensors drive the ignition timing, so the spark will occur when it is supposed to. It's not like the old distributor days when the ignition timing was done mechanically; then you could get 180 degrees off on ignition timing.

The gear has a key, but it can shear if the HB bolt torque is too low, and it needs major torque. Shops fail to meet the torque spec every now and then, if you follow the board for as long as I have. The same key does engage the HB, but only by about a quarter inch. So it is possible to install the HB without correctly engaging the nub, and then the whopping torque will just mash the end of the key. In either case, the HB time mark will not line up with the crank and give a false indication of good valve timing.

Did you have the HB off when you installed the new crank bolt? Could you confirm the key was intact and that the HB engaged the little nub end of the key? If so, then you are good because the key can't shear if the engine never ran. Still, one broken tooth on that sprocket can mess up the ignition timing.

This is not something that happens often, but you are running out of things to check.

EDIT: Sorry, I just saw you ruled this all out. As I recall, if you forget to plug in the MAF it won't start so no ohms can't be good.

Bingo! It was the timing on the Cams they were very very off most valves on both sides were opening at the same time. Got them back to the correct position and it started right up. Cant believe who ever had this engine before me would take something like that apart and not have the know how to put it back together properly. SO I get the cams timing correctly I left the intake Cams in. As they were already timed correctly with the timing belt to the crank. and took the Exhaust cams out on each side. I get it all back together and it starts right up. Almost immediately it starts to over heat -_- The water pump is new the thermostat is new the radiator is new the timing belt is put on correctly to spin the pump. I got all the air out of the system but still seems to overheat. Long story short its the head gasket -_- haven't got it apart yet to confirm but the air keeps coming out (its coming from some where) and you can hear the top end boiling over. This whole project has been a disaster. I spent 3 days changing the engine and a month trying to find issues and fix issues with it. But I'll know this engine inside and out by the end of all this. It has new head gasket on it you can tell from the outside SO I think the heads are just very warped. I'll update with photos when I get to the head gasket. Thanks for all the help everyone!

Oh and the MAF was actually fine I had a a general Toyota manual for all years and I didn't know this at the time but the pin out for the MAF changes over the years of the 3gen 4runner.

So...the person who you got the engine from, not only out timed the cams, but also had a potential head gasket issue and didn't tell you about it until it ran? Wow

Glad you were able to figure it out and got the 4r running.

Man good luck with that, it must feel like crap to be this deep into the rabbit hole because of the bad work of someone else. If at least he told you, you could have done the head in-situation before putting the engine in.

good luck, keep us updated.

Dang, that's really shady. I realize this is of no help to you now but when I was shopping for an engine I had them do a compression test right in front of me. A tip for anyone in the future reading this thread.

So not only did they super jack the valve timing. The engine had blown head gaskets. Man no wonder you can not get this engine to run. :-(

Glad you found out was was the issue. Timing. I am hoping now, you get the rig all patch up and rolling down the road..