One other quick thing I would check ... you mentioned you have not checked the tank. Are you still running on 7+ year old diesel fuel? If so, I would try running the car off Diesel Purge on a 2-liter soda bottle or the like and see if that engine quirk goes away.

See here for the howto: http://dieselgiant.com/injectorcleaning.htm

If you are running off the old diesel fuel, you are wasting your time with all of these steps until the engine starts getting clean fuel. I would be especially concerned about re-contaminating the injectors.

Dkr.