OK, that pretty much narrows it down. Remembering the basics: Air & fuel, compression, ignition & ability to exhaust.
Have you checked to see if the anti-shudder valve is open? I've never heard of it sticking shut but it's an easy check.
I know you've said that there is fuel coming out of the lines when you crank it but I'd confirm that the fuel shut off solenoid is opening and staying open. It's in the IP but I don't have the info to test it at hand (on vac in Lakeland). If you can, like mentioned above, hot wire it from the battery to bypass any possible programming issue or other fun Volkswagen circuitry.
The last thing to check is timing which you could somewhat inspect without timing tools. Pop the timing covers off and rotate the crank until the fuel pump timing holes are lined up. Then check to see if the TDC mark on the flywheel is near the pointer on the bellhousing. (that's the important one) Next, pop the vacuum pump off the end of the head and check the alignment of the slot in the end of the camshaft, it should be parallel to the valve cover surface.
If the pump and crank are aligned, the cam probably is too.
This isn't precise but it should give an indication of the timing being off enough to keep it from starting.
None of this has any association to the 1/2 tank issue. It might be worth checking for recalls on your VIN. Those can be checked here:
http://www.vw.com/owners/recalls/