PROBLEM SOLVED!!

To make this thread useful for anyone who happens upon a similar problem I will give a quick run down of what I did to fix my problem.

I replaced the cap/rotor/wires and plugs with genuine toyota parts and NGK spark plugs only to fine that I still had just 3 cylinders. I removed all the plugs to check compression again and did not find any problems. I finally decided that it could not be an ignition problem and finally turned to the fuel system.

I jumped 12 volts to the 3rd fuel injector and could hear it spraying fuel, I also check to make sure it was getting a signal from the ECU, everything seemed fine, however I still decided to pull the fuel rail. This really only takes about 20 min to pull the upper plenum off, once off I removed the fuel rail and the 3rd injector.

What I found literally looked like a brown booger oozing out of the fuel injector, I removed the rest to the injectors and clean out those and the rail finding more of this crap in the rail. It seems I either got a bad tank of gas, or some exsisting crap in the tank finally made it through the fuel filter. Using some carb cleaner I rinsed out the injectors and the truck is running well!!

I plan to change the fuel filter again and have the injectors sent out and clean again as they still may not be working perfectly