The screw on the back of the pump is not needed for TDI's since the timing is done electronically. If you have the dial indicator and adapter it will still work though in this application and might actually be a good diagnostic for you at this point since you seem to be in the "anythings possible" phase. You should set the preload off TDC and get the gauge to read at TDC just like before, this will tell you that the cam plate and plunger is timed properly to the shaft and the crank. Are you getting fuel at the injectors during cranking?
It's funny you mentioned the center pump head screw. My brand new ( from VW ) pump that I hung on my car last night was having a hard time priming with the mityvac, sometimes they do I think we can all agree... anyways, I got enough fuel into the pump to attempt a start and to purge the injector lines, I cranked it a bit and started getting fuel at the injectors, tightened them all down and was expecting it to start right up at this point. Nope, nothing, I did notice some fuel on things though, odd I guess I didn't clean up so well after the injector line bleeding phase. Tried again, more fuel... Hmmm, I guess fuel is coming from somewhere else... Sure enough, that center pump head screw was just finger tight from the factory allowing insufficient pump pressure to pop the injectors. Tightened it down and there she went... Took a while to get all the air out of the system on this one too despite having good seals at the filter, it seemed to just keep getting recycled and the pump was really foaming up the return line until a good 30 minutes or so of running.
Best of luck Warthog. I don't know what else to offer for advice, you seem to be doing the right things here.
BTW: The QA housing is VERY VERY sensitive, don't assume that you scribe marks will get you to starting territory, you may want to make some adjustements there, if this is the case, you may find that the engine will make weak attempts while cranking and speed up slightly but won't take off, this is everything working but just not enough fuel to support an idle speed.