Brightness adjuster not working

You have a bit of a misunderstanding here.
There is no "automatic" setting for the headlights. Well, except that if you do leave them ON, they will go off after a few minutes.

The "lowest" setting is all lights OFF, where the dash dimmer does NOT work.
The next click up is DRL......where the dimmer does not work either.
The dash dimmer only works with headlights or "parking" lights ON, which is the 3rd and 4th position.

 

The window has a don't-crush-my-arm feature programmed in, where if it is moving up and hits something, it stops and rolls down.

That, of course, can't be the whole story, because every time you roll it all the way up it hits something: the top of the door! If it didn't know better, it would hit the top of the door and say "oops" and roll back down.

... which is exactly what it does until it learns where the top of the door is.

When the window is replaced, it has to learn that again, and until it does, it behaves the exact way you described.

The process for teaching it the top of the door is roll it slowly up as you were doing and hold the button there for a bit. When that issue "went away on its own for whatever reason", I'm going to say that you unknowingly hit that combination right one time when you were rolling it up.