I took my 02 in to the Cummins shop that does all my installs to ask them about this sound (weird pulsation at 2k). I just wanted to make sure I wasn't hurting anything and it was due to the new airflow characteristics of the exhaust. Turns out I am the third guy with a 6speed that has had this problem. Apparently the VanAaken chip needs to be reflashed to conteract this noise. The guys at the shop felt that the autos probably exhibited the same problem, but the torque converter absorbed the frequencies. Truck goes in later this week, I'll post the results. Those running these boxes may want to call their distributer and cheeck into this to avoid possible hidden damages.
Matt
Matt