SJBrooks,
I, also, have an '03 (3500 HO, 6-sp. , 4X4) with a Van Aaken C 3. 2 (duration, only) box. It has 3 settings, stock, 65 HP. & 130 HP. I have a Magnaflow muffler & AFE PG-7 filter system.
I noticed while on the high level, with 3/4 throttle at about 2200 rpm, there is a "miss" that lasts for not quite a second. Apparently, it is a low fuel problem, from what I've been told. Doesn't do it on the 65 HP or stock levels.
At the 2006 May Madness, I put the truck on the dyno & at the 65 HP level, I made 341 HP at the rear wheels. On the 130 HP level, I only made 6 more HP (347 HP. ) My guess is that I reached the 'low fuel pressure' point on that run.
I know we are not comparing "apples to apples", here but, I thought you may be interested in my experiences.
From what I here, one of the upgraded fuel delivery systems (GDP, FASS etc. ) may be the fix.
Joe F. (Buffalo)