That is a shocker - dealer should have figured that out when you took delivery. The terms seem pretty clear, delivery by 10/4 - so that is not in your favor - even though it is not your fault. The dealer on the other had sold you the truck, you have a signed contract, they accepted the certificate, so likely on them to recover it - not on you.
Really gets down to is it worth the hassle to push back on the dealer? They did honor X-Plan, where many will not - so you did benefit there - if you are going to service with them, then your relationship value has to be considered over $2k.
I would ask to speak with the dealer GM or higher only to work it out. Be firm but friendly and see where you finish - maybe you pay the $2K, but think outside the box in what they give you in return - for example maybe they agree to sell you parts at cost until your $2k in parts discounts going forward is received (you pay cost on all parts until you get your $2k back) - something that allows them to not lose and you to get the value of the $2k. But don't spend to much time or angst on it - not worth it for such a small sum.
Good luck getting resolved and a favorable outcome.