Absolutely Stumped!

[sc6.0]

My problem started a few weeks ago after I got some water in my fuel. I replaced the filters twice and and things seemed as if they were going to be fine. I ran additives in order to help clear up the problems and hopefully prevent further problems. Then, it got worse. As I was driving, it would hiccup, blow a mix of black and white smoke and then accelerate normally, at least until I backed out of the throttle and began to apply throttle again, and the problem would start. It seems as if there is a bit of hesitation, almost as if the engine is not firing on all cylinders. The engine also sounds as if it becomes quiet, or nearly silent. I am getting good boost throughout the ordeal, and once it has its hiccup and blows the smoke, it begins to accelerate normally.
I believe it to be a problem with the EGR valve and EGR cooler. Funny thing is, when I change the fuel filters, it delays the problem slightly, but of course the problem returns. I unplugged the EGR valve and ran my truck for several days with no problem, just a check engine light. Yesterday, I plugged it back in and the light stayed on, and no more than 2 miles from the house, the problem started again. Do you guys believe I have this narrowed down now? Is it pretty obvious, or as obvious as it seems that it is the EGR valve/Cooler? Please, any advice or thoughts are appreciated.

[VeeDubTDI]

How frequently are you getting water out of the HFCM? It's pretty small, and if you still have water in the fuel tank, it'll fill up the water separator very quickly.

If water has made it all the way up to your injectors, you could be looking at some pretty big money.

Are you losing any coolant or puking? Have you removed the EGR valve to clean it?

Have you scanned it for codes to find out what the check engine light is for?

[sc6.0]

Originally Posted by VeeDubTDI

How frequently are you getting water out of the HFCM? It's pretty small, and if you still have water in the fuel tank, it'll fill up the water separator very quickly.

If water has made it all the way up to your injectors, you could be looking at some pretty big money.

Are you losing any coolant or puking? Have you removed the EGR valve to clean it?

Have you scanned it for codes to find out what the check engine light is for?

I have only had to drain the HFCM once, but I am draining it at least every two weeks.
I hope like all get out that it hasn't made it to the injectors, but I notified the the station where I got the bad fuel and they told me that they would accept all responsibility, but I have not heard from them since leaving a few messages.

As for losing coolant, it is a noticeable amount, but minimal and yes, I have cleaned the EGR valve, as it was not terribly "coked" when I cleaned it.
Finally, I have not had it scanned, but the CEL came on after I unplugged the EGR valve

[VeeDubTDI]

The CEL comes on on most trucks when you unplug the EGR, with a few exceptions (2003 included). If it runs better with it unplugged, consider an EGR delete kit and a new oil cooler. That will save you a lot of headaches down the road.

Are you puking from the degas bottle?

[sc6.0]

Originally Posted by VeeDubTDI

The CEL comes on on most trucks when you unplug the EGR, with a few exceptions (2003 included). If it runs better with it unplugged, consider an EGR delete kit and a new oil cooler. That will save you a lot of headaches down the road.

Are you puking from the degas bottle?

I have absolutely no puking from the degas bottle, only a minimal use of coolant, actually its negligible.

[VeeDubTDI]

Good sign that there's no puking or coolant consumption. If you don't feel like tackling the EGR delete project, then try replacing the EGR valve.

[sc6.0]

I dropped the fuel tank today just on a hunch that maybe there was residual water in my tank and when I hit bumps, my fuel sending unit was picking up water. So, as if I weren't having enough problem, somehow or another in the ordeal, I pinched one of the high vacuum lines...any suggestions on where to find this?