Hi gents,
While changing the front speakers on a 2007, I noticed a rectangular rubber piece about 6 inches / 3 inches wide, laying in the bottom of the door. Is this a component of the window power mechanism/rails? My window works perfectly, so I'm not sure what does this piece does.....

 

Sounds like you're talking about the Q pad manufacturers place on the inside of the doors. It's a sound deadener that you can place back in the door using 3m spray adhesive. It's typically placed in the middle or close to it. I'd recommend putting it back on, it definitely helps.

 

Sorry about the size, the vertical rubber strip that sits inside the front rail of the power window mechanism is what I'm referring to....this side slid half way down, the other door it came off completely. It doesn't seem to interfere with the glass action when is off but I can see it becoming and issue if it gets tangled with the glass when is rolling down...looks like is secured at the top with some kind of clip(which I can't find nowhere inside the door...)

 

I didn't pay attention to the guide/channel when I had mine apart. Most vehicles typically have two brackets with 10mm bolts that hold it in place. You could try moving it back and pushing the weatherstrip back in place. If you do pay attention to the dirt/wear marks on the door and place them back in the same spot when tightening. If not it'll change how tight the window is held, and affecting the lowering/raising. As far as the clip goes dealer/auto salvage.