The 2 I would recommend is:
East Side of the US -
Conestoga Diesel Injection - Mel (Agnem) yes, that guy right above this post. He is in Eastern Pennsylvania. I am in Central Indiana, and plan on sending the pump from my VW to Mel to get it "Tuned Up" and stop leaking. I have dealt with Mel on a few things, and have met him in person at a few rallys, he and Suzi are great to work with.
West Coast - Russ (typ4), he has a reputable pump shop he works with, and he and others have had a great deal of success with that shop.
A third shop is R&D IDI Performance. He is fairly new to the scene, and a few members here have used his "stuff" and have reported good things back from him.....