My dealer applied the MFT 3.5.1 this morning and had the A4 Nav. card to replace mine with. I will say few times I have driven since updating MFT, the problems I was having with Bluetooth Audio since upgrading to the iPhone 5 have disappeared and it does seem to run faster. As I was redoing my settings, I do not have to wait for screens like it did before.
I will also have to get props to Billy Howell Ford. They handled it quickly with no issues. It probably did not hurt my case when I showed the service rep a picture from last night that showed my phone was not connected to MFT but Bluetooth Audio from my phone was playing.