Every once in awhile it just hangs up and won't budge. Only way to fix is a reset with a battery pull. Lame.
My understanding is that you can get a USB fob from Ford that when inserted causes the system to reboot. It's keyed to your VIN so you can't give it to anyone else - but you have to ask for it from Ford.... I'd PM cory and see about getting one if you have to reboot it much.
I'm guessing you haven't repaired your phone, and if you have, you haven't downloaded your contacts. However, As for your phone contacts, you may want to reconsider the necessity of keeping all 6k contacts in your iPhone if you wanna use a telematics system like sync and have the phone book feature.
More specifically, transferring your phone book via bluetooth. The bluetooth used in your iPhone 4 (and MFT) is 2.1 mega BITS /second max. I did some quick calculating (hoping I didn't screw it up), but assuming each of your contacts is basic (2 numbers at most without email addresses or pictures) it's probably around 1kbyte per contact, with 6,000 contacts thats around 6 Mega BYTES of contact data. Just to transfer (no processing) all those contacts to MFT is
23 seconds (assuming max theoretical speed - which probably isn't going to happen). My guess is that it would be at least 35-40 seconds given that Sync appears to use an SQL server (which is horribly slow) and stores more info about contacts than your phone (voice command stuff). Add any pictures to your contacts and it could take all day to update. Assuming a 120x120 picture in horrible 256 bit color and thats 450kb which adds an extra 1.6 seconds at least PER PHOTO. 10 photos and you've got 16 more seconds. Add any better resolution or bigger size and you're gonna be needing the battery wrench. Those numbers are just for the bluetooth transfer portion assuming perfect network conditions which doesn't happen (ever).
Your MFT has to do this each time it starts up to see if there is a change in any data. This includes no processing time, which it then has to process each contact and do a compare against every field in the contact. Consider as well that its trying to load the navigation and your music and no wonder the thing is choking.
Additionally, my experience with Sync is that it doesn't manage memory very well - seems as if there are memory leaks all over the place. Probably what has happened LoganFilm, is that your contact list has probably exceeded the maximum size Sync had budgeted for contact lists and since it doesn't manage it very well - probably spilled over into some other area of memory which may contain data or code or what have you. Certainly not your fault, and hopefully fixed with the new S/W.
My suggestion is to see if you can download your contact list over USB. Anyone know if you can? That would be much faster, although it still wouldn't solve the issue if you are indeed capping the contact list memory size. Additionally, you may want to trim your contact list to the contacts you call most often, and store the other contacts in a text file or some other location - still accessible, but not downloaded by sync.