Car won’t start

Bought this car 3 weeks ago, ran like a scalded ape for a week! Cut the muffler off still ran fine, got around to straight piping and it ran fine all day. The next day I noticed it took a little while for it to start, did that all weekend. Monday rolled around took it to work, when I went to leave work it would crank but not start, so I bought a new fuel filter, o-rings, and re- primed the pump and she still would not start. Bought a new battery put it in there and it started right up. That night I went to start it and it took a while to get going again, the following day it would not start so I took the new battery had it tested and it checked out @12.7 volts. I was messing with the EGR anti shutter flap while my dad cranked the car and I held it shut for about 5 seconds and when I opened the flap the car sputtered then started figured the EGR might be clogged so I deleted it, all turnover still won’t fire up... a bit long winded, I have done a ton of research in the last 2 weeks but I have no clue what to do or look for as I am new to TDI’s

Following the how to above is necessary.
This it true even for the veteran TDI enthusiast. I will say that the 109 relay is a prime suspect, however, check for fuel flow first to rule that out. Then follow the link and run it down.

Appreciate the replys, I will look into it this weekend and get back with my results!

Alrighty, replaced 109 relay with one from ECS tuning plus got an extra. Re-primed pump and cranked injector lines and got the car started. Noticed a whole bunch of air bubbles in the clear lines I installed from McMaster Carr... any ideas where they could be coming from?

Check or replace the o-rings on the fuel filter/thermo tee.
You may have damaged or misaligned one of them.

The o-rings on the hard lines in the engine bay next if it doesn't stop. This is a suction line and will draw air anywhere it can. It'll draw air before fuel leaks out, so look at everything. Also pull the hose off the filter and stick into diesel bottle, or diesel purge bottle, to check that it's not a faulty hose letting air in at the beginning of the clear line connector.
Doing this should eliminate air bubbles and allow the car to start if that's what's preventing it from doing so.

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Been driving it for an hour and just got home, turned it off and immediately tried starting it again and it won’t fire up. Will look into the lines further

You have the infamous hot start issue it sounds like. The tuners build a fix for it into their tunes. Not sure what other measures there may be.

A couple to look over

http://forums.tdiclub.com/showthread.php?t=251287

https://forums.vwvortex.com/showthr...when-warm-after-driven#/topics/5573739?page=3

A long shot, but possible is a hairline crack in the fuel sending unit... in the tank... what is the fuel level in the tank? Mine would start fine when over half. As soon as i dropped below half full it would lose prime, crack in fuel sending unit.

Replaced the fuel filter with one from a 96 jetta and used a double male to join the return lines. Re-primed the pump let it sit for an hour and the fuel stayed right where I left it. Car started up and I drove it for 15 minutes got home and let it idle and noticed there was still a ridiculous amount of air bubbles in the lines so I shut the car off and watched all the fuel drain back to the filter.... car has been at right under half a tank since the problem started

Check the fuel tank sender.
I've seen this before. Some people try to do the cold weather mod and mistakenly remove the wrong check-valve. This would permit the fuel to back-flow to the tank .

Welp it turns out the stem that draws the fuel out through the sending unit was cracked and sucking air. Replaced the whole thing and now she runs pretty good. Thanks for y’alls input!