I have an HO on an SO truck. If you drove the HO truck without the Power Puck & the SO with the power puck in just timing mode (I think they can do that like the Edge EZ), they would seem identical.
Now, with my HO on the SO truck with the Quadzilla & COMP2 tune, I had to pull timing advance out of it in custom tuning to keep it from having a bucking at cruise.
Also, you have swapped your VP. I would suggest building a " Boost leak tester Cummins " to ensure that something isn't loose.
When doing your VP, you pulled bolts from the intake manifold plate. If it is the stock gasket, it is extremely brittle & may have cracked. Also, when putting ALL of those bracket, fuel filter bolts back in, you MUST use sealant, as they go into the intake plenum & WILL leak. If you haven't already done so, I would suggest pulling the 1st 3 or 4 lines (Look up intake gasket tutorial) & all bracketry to pull your intake plate. The 3rd Gen gasket is better. What I did was use the fatory gasket from NAPA & Permatex#2 gasket maker & glue the new gasket on the cover after FULLY cleaning & inspecting with a mirror for debris, put all of the bolts in the intake plate with the gasket tacked on & weighted down for 1 hour. Slide it back in. Bolt it back down woth the black or grey RTV (just a thin line down t a side of the bolt & reassemble. Also, you may notice (With said boost fooler) that you have leaks at the boots. See if tightening will help, or call Silicone Intakes for dirt heap priing.
Ed