There is a lot of good info in this thread: http://www.f150forum.com/f38/iphone-5-sync-207637/
However, Follow these steps exactly (props to @jgohlke
for writing all this out).
The sequence seems to have a large part of it working or not.
1) Truck - Delete phone from BT device list.
2) Phone - Delete Sync from BT connection list.
3) Phone - Reboot. (Do steps 4 & 5 while you wait for this to finish)
4) Truck - Turn off, pull the key, open the door.
5) Truck - Close the door, restart.
6) Truck/Phone - Pair your phone fresh w/MFT. Let it finish.
7) Phone - Turn BT off.
8) Phone - Turn BT on.
9) Truck - Hit "connect" on the MFT screen to reconnect BT.
10) Phone - Go into the BT Profile Settings screen for Sync (little arrow to the right of Sync, in Settings, Bluetooth)
11) Phone - Set Notifications to "On".
12) Phone - Back up a screen and turn BT off again.
13) Phone - Turn BT back on.
14) Truck - Hit "connect" on the MFT screen again to reconnect to phone.
I did exactly this to my phone/truck when I was trying to fix my text messaging issues. I haven't had a problem with it since.