The only issue I'm left with (and this may not even be an issue since the car only has 800 miles on it) is that every once in a while, it will shift funny when accelerating from a dead stop (from a stoplight/stop sign). But the majority of the time, it shifts fine. Maybe is't just me, or maybe some things still need to wear in a bit...
Prior to taking my car in, I told the dealer that I would give them a fair rating based on the level of service I received. Needless to say, I will be giving them a good rating for taking care of the bearing issue in a somewhat timely manner. I just hope my trans won't be needing a replacement like yours was. Hopefully the issues i see are just a matter of time for things to wear in. I actually haven't driven it a lot on the highway (at least not for any more than 50 miles at a time, so maybe it needs to be run at higher RPMs for a little while or just be flat out driven more. I'm going to wait until 1500-2000 miles, and if the problem doesn't go away, I'm going back to the dealer.