1) Either it's the sub or the "mid" speakers in the door trying to boast too much bass therefore distorting the sound or they've been torn. easiest way to decide whats busted is use the bass knob with fade\balance adjustments to figure out which speaker is making the noise (will need to be replaced, no real fix).
2) Dont know how you can tell, but it is okay to mix the two if they used synthetic.
3) Get a flashlight and crawl under your dash by your pedals. I would assume that there may jsut be some linkage on the cabin side that needs to be adjusted\lubricated. I could be wrong, but I'd check that.
4) Your master key will be the master key no matter what (im pretty sure) adding other keys should not affect it, thought Im no expert in the key dept.
5) Never done it but I think you needa special tool and to be very careful with the airbag as to not deploy it. Ive taken the easy way out and covered it for now.
Sorry I cant be more help - I did what I could tho :)