2004 Audi A6 3.0 190,000miles
Did a timing belt etc about 10K miles ago. No problems since.
Driving 40 MPH and the car started missing, moments later the check engine light started blinking. Drove a mile and pulled over. Let it sit for 30 minutes and started it up...hard start and missing still. Flatbed to my garage. Ran the VAG and got the following:

VCDS-Lite Version: Release 1.2
Wednesday, 30 October 2013, 19:07:25.


Chassis Type: 4B - Audi A6 C5
Scan: 01,02,03,06,08,15,16,17,18,22,34,35,36,37,45,55,56 ,57,65,67,75,76,77

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Address 01: Engine Labels: 06C-909-559-ASN.LBL
Controller: 8E0 909 559 R
Component: 3.0L V6/5V G 0010
Coding: 0016752
Shop #: WSC 02325
VCID: 44FBCF134783
3 Faults Found:
18032 - MIL Request Signal Active (Check TCM for errors too!)
P1624 - 008 - Implausible Signal
16684 - Shareware Version. To Decode all DTCs
P0300 - 001 - Please Register/Activate
16688 - Shareware Version. To Decode all DTCs
P0304 - 001 - Please Register/Activate
Readiness: 0110 1101

-------------------------------------------------------------------------------
Address 02: Auto Trans Labels: 01V-927-156.LBL
Controller: 4B0 927 156 FF
Component: AG5 01V 3.0l5V USA 0910
Coding: 0001002
Shop #: WSC 02325
VCID: 709353C323BB
1 Fault Found:
17125 - Torque Converter Clutch: Stuck OFF / No Power being transferred
P0741 - 003 - Mechanical Failure

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Address 03: ABS Brakes Labels: 4B0-614-517.LBL
Controller: 4B0 614 517 H
Component: ABS/ESP allrad 3428
Coding: 06497
Shop #: WSC 02325
VCID: 263F759BD1FF
1 Fault Found:
01435 - Brake Pressure Sensor 1 (G201)
48-00 - Supply Voltage


I knew about the torque conv. problem but everything else is new. Checked some forums and they recommended coil packs. Replaced all 6 with new coil packs. Same problem. Spark plugs were new when I did the timing belt, but swapped cyl 4 and 5. Same problem. The last time I started it, it took about 15 seconds to catch and the big red engine light came on for the first 2 seconds of the car running. I am freaking out as I just sunk a ton of money into the timing belt repair. I don't know where to start looking. Any suggestions? Thanks!

 

Did this big red engine light appear while you were driving or while you were at idle? This could have been a low oil pressure indicator light...

 

Red engine light came on for a couple seconds after the latest hard start, then went out right away.

 

I swapped #4 and #5 fuel injectors. Reset and restarted. Same codes, same missing. Anyone have any other ideas? I have read about harness problems. Is there an easy(easier) way to check that?

 

I would check the compression on all the cylinder & see what you get. You could have a dead hole.

 

UPDATE - ran compression test as suggested by M5S5. Here are the disgusting results:
1 - 115
2 - 120
3 - 100
4 - 0
5 - 90
6 - 95
So, I have a dead cylinder...what next?

 

Leak down test to see where the leak is. This will tell you for certain where your leak is. You will have to get the crank at TDC on that cylinder during its compression phase to run the leak down test. This is kind of tricky if you have a 0 compression condition on the cylinder.

I'm not sure of the firing order of your engine, but if cylinders 4, 5 and 6 are on the same bank, then I would lean towards a head gasket being the cause for loss of compression given the fact that those compression results are vastly different than cylinders 1, 2 and 3. Do you notice coolant in your oil?

 

What is the technique to get the cylinder at TDC? Will check oil in the morning...I do remember noticing the coolant reservoir lower than it should be now that you mention it.

 

Here is a pretty good video on the procedure:
Of course, I think he's doing this on a Chevy engine in the video and things aren't as easy on an Audi. Note that if you have 0 compression you may have to rely on the cylinder just prior to the suspected bad cylinder to determine its position in the stroke cycle.

 

No milky oil, doesn't look like oil has any coolant in it. Need to rip the head off. Is there any DIY on cylinder head removal (drivers side)? I can't seem to find anything useful. BTW..just stripped out 2 crank pulley bolts. They probably should have been replaced the last time the timing belt was done. Now I have to pull the front end completely off to get a drill in there to tap them out!!! SO FRUSTRATING!!!