Opened a whole new can of worms.

[A4Mods]

Well, apparently my OBD II scanner is a piece of junk. My car's had a rough idle on and off for some time. It's not consistent at all. Sometimes it goes away entirely, however it's usually there. Sometimes worse than others, I grew use to it though.
Anyways, for the first time in the two years that I have owned my car, it died on me. As soon as I got it I started replacing everything that I didn't have records of being replaced and that people claimed to be common problems. Anywho, when it died leaving work, it shook violently. I was able to get it to start back up by feathering the gas while cranking the key. It started, although it obviously didn't want to. I work a lot so this is the first time I've been able to sit down and actually try to figure things out. (Although I should be in bed as I just got off work and work another 13 hours tonight)
My scanner only showed me two codes.

I assume this one is due to a gutted cat.
P0420
Catalys System
Efficiency below
Threshhold bank 1

I assume this is due to removing the secondary air pump.
P0411
Secondary Air
Injector incorrect flow

Then my buddy used his scanner, and came up with these....
P0638
Throttle Actuator
Control Range/Performance (Bank 1)

P0122
Throttle/Pedal Position
Sensor A Circuit Low

P0222
Throttle/Pedal Position
Sensor/Switch B circuit low

When the car died, I right away jumped to the fuel pump, as it was exactly what happened in my 2002 VW jetta.
Considering the fuel gauge sending unit on mines been toast since day one, I didn't mind buying a new fuel pump, whether is solves my problem or not.
Also considering when I changed the fuel filter, the gas in it was thick and black and resembled used motor oil more than gasoline.....
Anyways, while I was at it, I figured I might as well replace the injectors too. So I bought motoza Stage 1+ with the Bosch 550CC injectors.
All these should be arriving sometime this week.

List of things I have done to the car since I purchased it.
034 Snub mount bushing
034 Engine Mounts.
New MAF
New Throttle Body
New Diverter Valve
N75 Race valve
New crank case breather tube
Fuel filter
Spark Plugs (Changed them twice, both with OEM plugs from the dealership, came pregapped but checked the gaps before installing)
Vacuum simplification mod (Found on these forums)

The cat was gutted when I got the car, I plan to change it to a test pipe soon. I'm assuming it was gutted due to being clogged, or someone didn't want to buy a test pipe?

TLDR VERSION!!!!
Most common issues that would throw these codes?
Rule out the part's I already replaced.

034 Snub mount bushing
034 Engine Mounts.
New MAF
New Throttle Body
New Diverter Valve
N75 Race valve
New crank case breather tube
Fuel filter
Spark Plugs

[Seerlah]

Did you do a throttle body adaption with the replacement? Key in ignition won't cut it here. You need to do a full TBA with appropriate software. And that MAF was Bosch, correct? Did you do a boost leak test?

[A4Mods]

Yes, it was done at a local APR dealer just across town.
Also did a boost leak test. Came back good.
Had a leak down test done as well, all was well there.
The MAF I bought at the dealership, factory replacement.

[Seerlah]

Weird. Only thing I can really think about is the crank sensor. It makes the car act really strange before it shows any signs of it being the culprit (ie no DTC till right before it goes out, but nothing prior to). You should scan for intermittent codes.

[A4Mods]

Crankshaft position sensor is what, like $50? I don't mind replacing it for shits and grins in hopes that it helps. Lol.

[Seerlah]

Yeah, they are fairly cheap. Bosch online is a good $20-40 less Autozone/Advanced Auto behind the counter stuff. Go figure!

[A4Mods]

Yeah, they are fairly cheap. Bosch online is a good $20-40 less Autozone/Advanced Auto behind the counter stuff. Go figure!

I'm thinking maybe with the snow outside, moisture got on the sensor that's apparently on the pedal? I can't find anywhere that sells just the sensor, infact I can't even find the exact pedal I have and I don't watch mismatched pedals...lol. I can find the pedal with sensor for the B5 and for VW passats.....Any ideas?

[Seerlah]

What sensor are you referring to? Crank position sensor and engine speed sensor are one and the same, and located on your engine block behind the oil filter.

[USAF Long]

I think he's talking about the throttle pedal sensor or throttle position sensor. Is it located on the pedal assembly?

[A4Mods]

I think he's talking about the throttle pedal sensor or throttle position sensor. Is it located on the pedal assembly?

Correct. From researching the codes, I came up with that as a highly probable cause, as well as possible moisture getting to the ECU throwing the same code, and come to think of it. This all happened the day after a car wash.

[Seerlah]

Throttle position sensor is on the throttle body itself. If faulty, whole tb is to be replaced. Can be scored for cheap on eBay.

I'm not fluent to the pedal sensor, and hopefully someone chimes in for info. But that sensor is different than the throttle angle/position sensor found on the electrical section of the throttle body.

[A4Mods]

Well, I've actually had that code for a long time. So like I said, I replaced the whole throttle body. Brand new one. I purchased my code reader at the same time........Once I installed it I still had the intermittent rough idle, but the code reader I bought wasn't showing that code, so I thought the brand new TB fixed that and it was something else. All the existing vacuum lines and valves where replaced when doing the vacuum simplification mod.
My buddy was just here with his code reader again. We took the car for a drive and nothing happened.....cleared the codes and drove until the CEL came back on to see if it was throwing any other codes. Nothing new, same codes as listed above.
I'm wondering if the ECU isn't sending that code for the TB sensor for some reason. Once we got back from driving around, I came home to a nice surprise. The new fuel pump has arrived!!! I'll wait until tomorrow evening to see if my stuff from Motoza comes and install the fuel pump and injectors all at once. I'm really hoping to get this all sorted out so I can buy my coilovers, F21L Mixed flow franken turbo kit and FMIC, and other goodies. After that I'll probably start working on customizing the interior. A pillars, roof lining, B7 center console swap. (Maybe even a B7 front end conversion?) Anyways, this has to get sorted out before I begin modifying the car more.

[A4Mods]

Still no resolved to this issue. Any other ideas?!?!

[Tanzimur]

Any update? struggling on a buddys car same exact routine as you went through...