So some of you may be wondering how this situation resolved, well, it's not quite how I would have liked. Acura classified it as a "warranty repair" and took off 20% of the final price. The final cost to replace the transmission and the computer came to a little under $3700. That's a long way from my request that they cover at least half, but the almost $900 off is better than paying full price.
I have been trying to get in contact with the client care reps to discuss my "satisfaction" with my service. I don't really expect that will make anything better, but at least I'll get some closure on being able to express my disappointment.