OK.. just confirming that you've walked through the procedure of the FSM - not just stuff that people have recommended.

The FSM that's posted does have those pages.. A few notes:
Info on trouble codes for the V6:
http://personal.utulsa.edu/~nathan-buchanan/93fsm/engine/85diagnosi.pdf



Troublehshooting the IGT is in this section, but it requires the truck to be at idle.. So I really don't see how it's useful..
http://personal.utulsa.edu/~nathan-buchanan/93fsm/engine/86troubles.pdf


Here's how the system works:
http://lakebox.dnsalias.com/photos/1988%204runner/megasquirt/toyotaVAST.jpg


I'd want to know if I get a 5v square wave out the IGT pin (leave the harness connected to the ECU) when cranking. This will most likely show as a 3-4v indication in a voltmeter.. or maybe a swinging indication of voltage on an analog voltmeter like you're using. Test IGT between the pin and ground.
No IGT = No spark.

No IGT could be caused by a bunch of things:
1) Bad pickup on the distributor.
2) Bad Ignitor.
3) Bad wiring between the distributor and the ECM.


You should also check the input on NE at the ECU, again with the ECU plugged into the harness, based on my VAST diagram. It's 12v square wave for the 22RE.. I *think* it's the same for the V6.