Well, it took 2 days, but the dealer finally got back to me with the results of their testing and prodding. Turns out there is a broken plastic T causing a vacuum leak. Problem is that its in the intake manifold. $200 repair. While they were at it, they found the turbo oil return tube seals leaking again. Warranty will cover that, but not the vacuum leak. I still can't figure out why the warranty covers things I think shouldn't be covered and doesn't cover things I think should. Anyway, they said everything else is good and works great. They will document my concerns with the rough transmission shifting but it checks out ok for now (of course, I knew they'd say this, but just wanted them to document it anyway).