Personally I would've worked on making it run before modifying the stock setup with things like the EGR delete as now you've changed the rules of operation on a car that already wouldn't start on its own...
If I read things correctly, car was running, turbo failed miserably and caused the car to run bad, almost catastrophic.
Turbo got replaced and somewhere in that mix I read about the injection pump also being replaced but not sure why, and now the engine won't run via the fuel system.
Is all of that about right?
If the injection pump and injector lines haven't been bled/primed the car won't start.
If the injection pump was replaced and not properly timed and quantity adjusted the car probably won't start and can be so far out that it won't even cough or sputter or anything.
If you crack the line nuts loose somewhat on the injectors and crank it, does it make a fuel mess or do they stay dry? If you crack them loose and don't get fuel everywhere during cranking then the pump isn't primed, at the least, or the quantity adjustment is very wrong, assuming pump timing is even correct.
Seeing if you're getting fuel at the injectors is the easiest place to start.
Totally forget everything you know about gas engines and their various fuel delivery systems. Diesel is totally upside down and backwards in comparison, depending on your perspective of course...
Also note that although an ALH is usually running within a couple rotations of the starter or less, almost instantly under normal day to day circumstances, it takes a lot lore cranking on an unprimed ALH than you'd probably ever try on any gas engine to get it to start for the first time after prime loss. If you haven't gotten the oil pressure warning light and buzzer at least once already then you probably haven't cranked it nearly enough to re-prime it yet, although that's a good stopping point to let the starter rest a little before the next try.
A Mity-Vac (or equivalent), a line or crescent wrench, a vag-com, and a hammer can be your best friends with many ALH "won't start" issues.
There's one of each in the trunk of my '01 Jetta at all times.
Unfortunately my KII-USB vag-com cable doesn't speak CAN-BUS which started in 2003 so it couldn't help for your situation.