We just got our Navigator back from the dealership, a total of 4 weeks there. My experience has been extremely frustrating with the dealership. Very hard to communicate with them, had to get corporate involved and was assigned to a very pleasant rep, the rep's even had a hard time communicating with the dealer. Spoke to service director, and he promised to have a body shop that is certified to work on Lincoln fixes the gouge/dent that some idiot there caused. I track the car daily via Lincoln Way app and saw that they dropped the car off at some random no names to do the body work. I can see where they did bondo and the blending is horrible. To keep it short, for engine noise they replaced the camshaft and sprockets, its still too new for me to see if the loud noises still exist. They found no exhaust leak even though i told them where is the leak and show the SA a video of the leak. No resolution for the mirrors yet. Now my other screen for the entertainment is not working, was working fine before dropping it off 4 weeks ago. They're going to replace both instead just one, just have to wait because of backed order. I truly expected alot better from Lincoln, since there are very few dealers in my area, I dont have much options. I've owned numerous cars from many manufacturers and i can tell you that Lincoln is far behind on the their service level wise compary to others luxury brand.
Tell your dealership to look into your navigator to check for any codes and diagnose to see if the noises are related to camshaft/cam phasers.