Another update:
Surprise, surprise... CarMax has officially declined the tranny repair claim (they will cover the water pump) stating that a technician at Jerry's told them that the clutch caused the damage!

Well, CarMax is a bunch of bold faced liars because 5 minutes before I called them to find this out, I called Chris at Jerry's and he told me that the reason the tranny is grinding is because the blocking ring is broken causing the gears to spin simultaneouly when I shift. Not only did Chris not tell the CarMax inspector that the clutch caused the problem, but he showed the inspector the broken ring, demonstrated the grinding, and told me that it is impossible for the clutch to cause the blocking ring to break.
When I called CarMax I told them that their inspector was lying, so now Chris has to call CarMax to explain the real reason why the tranny in malfunctioning which is fully covered under my warranty.
Why do these corporate bastards make everything so difficult!

If they keep refusing the claim I am not only going to take them to arbitration, but will let them know that they have made a customer relations mistake because I plan on letting the 8000+ members of CEG know that their warranty isn't worth the paper its written on - Hurray for the internet and the power of instant mass communication!