Haven't touched a gen 2 but assume they are still using the same barrel to shroud support and cone-shaped baffles as the gen1. I never had an issue with clipping, but did notice how fragile the aluminum air cylinder to shroud barrel band was, and how easy it was to strip the set screws if not careful. I would check that when attaching the barrel band you are not accidentally getting the shroud skewed in relation to the centerline of the action and air tube. If skewed it will throw your shots left or right and can affect vertical poi.
What happen if you remove all the baffles and the spacer that goes over the narrow part of the barrel and put the end cap back on? Are the pellets clipping the end cap? It seems something inside the shroud is pushing the barrel off center.
Is the muzzle on a DAR barrel threaded?
The shroud support that slides on the end of the barrel. How loose is it on the barrel? And how loose is it in the shroud? I suspect bother are a little on the loose side causing your problems.
It looks like the rear shroud mount slides over the barrel and is secured with grubs. How sloppy is the fit on the barrel. Remember, a little off on the back of the shroud is a lot off by the time you get to the front.