There is a connection under the dash, I unplugged it and ran a resister in the computer side with the resister linking the 2 wires together. From what I found on the site this bypasses the VATS, I don't know much about electronics on cars! So I can't go into detail, but when I did it wrong the first time, car would not even crank.

 

I see.
As a cross-reference, a 98 needs the ign key, or, as you did, replace the key with the proper resistance value.
After the key/resistor is turned, a BCM (body-control module, located in the pass side/ kick area) receives from the key-side circuit, and the BCM then sends a (300 hz) signal to the computer, to start the engine.
A VATS bypass module (aftermarket) will mimic the 300hz signal (which eliminates the need for a resistor key, and the BCM) and allow the engine to start.
The alternative to the VATS bypass, is to turn off the VATS system, itself.

 

I was told it can be dissabled with HP tuners, but this don't even seem to be effecting my issue.

 

Your problem is that the PCM is not reading an engine RPM. VATS or no VATS if the PCM does not read any engine RPM it will not fire the injectors or plugs.

 

You don't have the cam and crank sensor connectors swapped by any chance do you? I believe the connectors are identical aside from the wire colors. Not sure if they can be swapped and connected to each other.

 

In my case, if the engine is not enabled with the correct VATS conditioning, the computer won't read anything, at any time.
I'm not saying that this is his problem, but am trying to decipher some information which has not been made clear.

 

My buddy came over with hP tuners, some reason my scanner was not showing po335 any more but it's still there! The tuner showed no signal from crank sensor still! So has to be a bad wire right?

 

I would say yes. Do a continuity test from connector back to pcm to see if the wire is good.

 

My rebuilt Lq4 with 500 miles would start and run just fine but if I shut down to restart when warm sometimes it would do the same thing your saying. In eflive I would get no reading on crank sensor. I emailed Justin at black bear and he told me my crank sensor should be whats causing it not to start as my log file was not showing any RPM when cranking over. Long story short he sent me a new computer with updated tune and it has started every time with no issue. I seen you changed that out already so unsure.

I know not the same problem but could be similar. He also sent paper work that I have now lost saying that if no start leave key in the on position for 30 min. Try to restart and if failed do up to 3 times for ECM to learn something(sorry dont know what its learning). Mine started every time I switched ECM so sorry no more help.

Good luck

 

Before you replace any more items, verify the continuity of your crank sensor leads, from the pins of the plug, to the ECM pins.
Visually inspect the crank sensor pins.
Verify that your grounds are good.