Okay, update.
Got the intake manifold completely off. I hate how they attach wiring harnesses to multiple separate parts.
Then after searching, studying, searching some more, I finally located the crank position sensor. It isn't where it's shown on the wiring diagram lol. It's actually under the engine whereas the diagram shows it as up-top. It's basically behind the AC compressor. Brutal to access. I probably could have avoided pulling the intake but it gave me a bit more room and since there are 2 broken harnesses and some rotted hoses up top it's worth refreshing.
Anyway, I managed to get the clip that holds the crank position sensor harness in place ahead of its termination off. barely. you have to do it completely by feel, pull up on the tab and then pull the clip back..where it bumps into something else and can't be removed. The trick is to basically manhandle it upwards a bit. Fun stuff.
As for the sensor connection itself, I have to remove the driver's wheel, serpentine belt, and AC compressor (yeah). I ended up using my SxS to drag the 4runner up hill from its parking spot and managed to push it into my workshop so I can do the job as this isn't happening on gravel.
Hopefully get that done tomorrow in the cool morning weather, and then redo the other connections. I think the wiring below the exhaust that is damaged is still making a connection so I'll find a way to cover it with new split-loom and pray. Then it's reinstalling the intake and figuring out all 900 connections on there.
Absolutely brutal job.