The factory wheelbase difference between driver and passenger side may be what you are noticing.
Was it an alignment printout that says the thrust is out, or your tape measure?

 

Tossed in a powertrax locker in the front and it just does not seem to be engaging. When spinning the tires you can see the teeth skipping. The center shaft is also very loose but that seems like it's supposed to be. What could cause it to not want to lock? I've tried doubling up in springs but still nothing

 

Troll? Did you try spinning them by the driveshaft? That's when it locks...not by spinning one of the wheels...

 

Sounds normal. With one wheel on ground, the other wheel will turn by ratcheting the locker.
Also, if both wheels are off the ground and the transfer case engaged in 4WD, when you try to turn one wheel the locker will ratchet.

As for the cross pin, when drive torque is applied, the crosspin 'engages' and locks the ratchets by preventing them from opening. Additional spring strength may cause issues with this balance.

 

That's the thing I put it in yesterday and took it offroad, when I got into some mud neither front tire would spin and you would hear the clicking so essentially I was 2wd

 

Is the gap in the locker in correct specs?

 

The center-gap does look big on the pic you posted.
My Aussie locker has two gaps that must be measured and within a specific range to function properly. And it uses the stock thrust washers.
And, are you certain that the transfer case was fully engaged?

 

Could it be that I'm using the stock center shaft install of a hardened one? The hardened ones I've found seem to not have the bevel and that almost seems to be giving too much travel in the locker

 

My stock center shaft is super tight in my Dana30s powertrax.
But I say you check the gap. I had to add some pinion shims I had laying around to tighten the gap up in mine. My problem was that the locker was always locked

 

Yeah see my shaft is very loose, maybe 1/4 side to side motion. Gap where?

 

I agree to start with the gap.
Was it measured and within the specified range? I believe this is the key.
I presume you have an installation guide with the tolerances and where/how to measure it?

 

Unfortunately it didn't come with instructions, do you remember the measurement?

 

Google them up, I can't remember exactly but yours looks too big.

 

That's what I thought too but the only way to fix that is more shims?

 

Yep. Also make sure in each pin hole you have a small spring in a bigger spring