For the front speakers i would change the 4x6 to a 5 1/4 or 6 1/2 which ever you like better. For the rear 6x9 you could use an adapter plate to mount 5 1/4 or 6 1/2 back there as well. As far as brand there are so many that i would say go listen to a bunch in peoples cars and go from there. I personally like the Memphis Mclass for the speakers. Good luck. As for the cleaning up the sub you got me on that one. You might just pop test (hook up speaker wire to the + and - of the woofer and the put the leads to a 9 volt battery to see if the woofer moves) and meter them to make sure they are good.