You can find the activation codes on eBay, if you want the factory nav. I used this one and had the code about 5 minutes after I sent the seller the request code. 5 more minutes to activate in the truck.
https://www.ebay.com/itm/204318852548
Had the same problem just before Christmas, and the same dealer in McKinney replaced my intake under warranty.
I've had really good service from them even though I bought my truck used from another dealership.
Same story as the OP, 2015 Ecodiesel 135k miles, and I also just got a new manifold due to the swirl valve. Is the GDE compliant hot tune worth it with 135k already on the odometer?
They have them on sale right now with the transmission tune for $995