I have it on my 2022 BL SAS and love the changes. It only takes about 20 - 30 minutes to do the install. You dealer is ripping you off find a Ford certified tech to do the install.
I completely removed the B & O amp and put a Axxess DSP in, the Kicker 800.1 on the sub enclosure, added 2 Euphoria amps (1 under each front seat) for the other speakers.
I would first check to see if all the latches are in the full close position, however if they are I would take the front section off and reinstall it. If that doesn't fix try the mid section.
Most likely the window is out of sync and doesn't go down when you open the door. It's riding on the outside of the gasket at the top. Correct by putting the window completely down and hold the button for 10 seconds then put it up completely and continue to hold the button for 10 seconds it...
I used a kicker 800.1 amp with a 8" kicker low profile sub in the stock enclosure. I had the B & O system but replace it with 2 additional amps for all the other speakers. Tied it together with an Axxess DSP.