From your description of wind noise and shudder it sounds like you have multiple problems because you're mentioning transmission, tires, and weatherstrip. The transmission shudder is mainly on the 8 speed but can happen with the 6 speed as well. The 8 speed has multiple updates including programming and a new fluid composition.
Just because the tires are new doesn't mean they're good. What kind of tires are they and what size? If you don't have Michelin Defenders, that's probably a big part of your problem. These trucks are extremely sensitive to tire roundness and the larger the wheel the more sensitive it is. The roadforce has to be perfect and if not then the tire(s) will have to be replaced. There are also updated steering gear bushings that make a huge difference in vibration.
The body booming is something totally different as well as any wind noise or noise from the window motors.
Just because the tires are new doesn't mean they're good. What kind of tires are they and what size? If you don't have Michelin Defenders, that's probably a big part of your problem. These trucks are extremely sensitive to tire roundness and the larger the wheel the more sensitive it is. The roadforce has to be perfect and if not then the tire(s) will have to be replaced. There are also updated steering gear bushings that make a huge difference in vibration.
The body booming is something totally different as well as any wind noise or noise from the window motors.