I spoke with the dealership, and GM this morning. The dealership says that it is GM policy not to warranty any of it if engine components have been changed out with aftermarket parts. Oddly enough, GM customer service said that IS NOT the policy. The dealership says they have to get it in and diagnose it first (understandable) but have already said that they won't cover it even if they find that the mods have nothing to do with it. Good to know they are willing to go in objectively, right? They want $100 an hour to diagnose it, and they are saying $1700 to fix it. This is what they tell me even after GM customer service calls them. At this point, knowing that I am dealing with dishonest people, I'd rather just pay the performance shop the $600, get a better pump, and know that it will be done right.
Way to go GM!