I removed my upper intake on my S engine to open up the webbing and add a boost guage. What I found inside is awful. There is at least a 1/8 of soot and gunk on both the upper and lower intake. Cleaning the uppertake is not a problem. Is there a way to safely clean the lower intake without removing it? I was thinking of wiping it out with a towel and then vacuming, but I am concerned about this gunk getting in the engine.

Pull the lower intake, wash it with Diesel fuel - don't get any of this mess on you - then full scoop of laundry detergent to 4 gallons HOT water, scrub and rinse.

However, your "S" engine will do it all over again, soon - that's exhaust soot, from the EGR system.

If you block off your EGR with a metal gasket, you will never have a soot problem again.

Burk update your sig per welcome notes suggestions in sticky threads http://www.dieselplace.com/forum/showthread.php?t=19063 at top of 6.5 header so we know what flavor GM you are driving.

Would plugging the vacum line to the EGR accomplish the same thing?

Possibly set a code not sure with OBDI PCMs, and if you have a weak EGR valve spring, valve can leak EGR gasses by, especially once you start building for more power