Wheels & tires are new and it’s not coming from the tires. I can feel it directly under the drivers side floor board and gears 2-3. The sound deadening is loose directly underneath the floorboard so I wonder if that has to do with it? There no buzzing gears 4-6 and it’s more prominent when the AC is on. No CEL. Other than that truck is perfect.
While you are under there, take a look at the factory tape that covers up the holes on the inside of the rockers where the running boards bolt onto the truck, if the tape is peeling back and stuff, rip it all off, clean the area really well and let dry totally, then add new black gorilla tape on there. A lot of us have done that over the years, since you're new to the raptor, it may have been done by a previous owner, but most haven't. If mud and debris gets in there, it clogs up the drain holes in the rockers and they will rust out. Hope you fix the vibration as well.