Sounds like it requires a load and I am not familiar with what a CP3 knocking would sound like but I would guess it has something to do with it. Turbo's won't build up much pressure without a load either so you might want to focus in those area's. Check your drive train as well I guess. Parts of the truck will act differantly when you apply a load to it so check out everything you can think of that might change during a load. Try hooking a heavy trailer to it and pulling up hill slowly to check for the knock. Maybe even try some power breaking without letting the tires loose and see if you can hear the knock.
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'04 3500 Laramie SB QC 4x4 305/555 CTD, 48RE, AFE Stage 2 CAI, 4" Aero 4040 Turbine, Banks Six-Gun w/PowerPDA, Tone Ring Mod, 35/12.50/17 MT Baja Claw Radials, 2" Leveling Kit