Short and sweet:
1) Don't buy the truck, even with a substantial discount!
2) Don't buy the truck unless they fix it the way you wanted and ordered it (and if you can live without the Nav. thing, which I agree is silly since it delays boot time and your abilities to use the backup camera)
3) Don't buy the truck and ask them for a few perks (oil change, etc...) for ******** up and wasting your time!
They are more likely going to make MORE money out of ******** you over than they would with your pre-order. They now have an available Raptor on site and will ask a premium (either MSRP or MSRP+) to those who are not willing to wait..... so they can "pay you" for ******** you over. Remind them how long you waited and how long they had your deposit?? Time is money!
If you really want to play hardball, send them a REGISTERED letter telling them that they have x amount of time to rectify your order, or be subject to legal action. A purchase contract is a legally binding agreement, which they obviously failed to fulfill. Once they've accepted your money they are obligated to complete, or be subject to fines and penalties. Any judge will side with you on the fact and will be glad to give you the deposit back and additional moneys to pay for court expenses, time off of work and can even go as far as giving you emotional distress and punitive damages (depending on how the dealership is willing to accommodate you).
You should not be asked to compromised, and should not be required to reset your wait time without just compensation (in the form of a discount on the purchase or in the form of perks like oil changes etc...). Your lost is their gain, trust me and they should not benefit off your back (which they will).