New to the trucks, but on everything else i've ever lowered, the bumpstops are not supposed to be "ridden" on. If im right that this assumption applies to our trucks, then it is absolutely the cause of a harsh, terrible ride. the bumpstops limit the travel of the suspension, your truck sitting on them at static heaight means your shock/spring are barely carrying the load, instead youre relying on those hunks of vulcanized rubber to soak up bumps. The techs at the alignement shop probably have the truck on a lift when they inspect it, this allows the suspension to droop, thus its pretty difficult to identify that issue under those conditions. trim the bumpstops and see where youre at then.