No harm in trying it mate, these older Alpines are still great units
(A shop will charge a few quid though especially if the start ripping the interior out and route cables etc as it takes a while to do properly, try to DIY, its not that hard once you get into it)
What I'd do is run the components off one amp (the better one of the two, what brand are they btw? & what channel? ) then run the sub off the other from the head units RCA sub output. Just fit the rear speakers and run off the head units rear speaker outputs but keep them faded out unless you get rear passengers otherwise it'll pull the sound stage to the rear and muddle up the sound (sounds horrible & echoey)
Try the JBL sub and see how it sounds, the Focal might not be a straight swap as they tend to come in odd sizes (11" & 13") instead of the usual 10" & 12"
What Focal sub is it? I've just sold one! Should have really kept it
CDT are a very good brand
I've never heard Polk but they're popular in the states and also very good.
Should sound nice mate! Definitely worth sound deadening to cut down on road noise & vibrations (makes a big difference if your after a SQ set up)
I wouldn't bother with Dynamat though as its well expensive, Silent Coat does the job and is around 1/2 the price!
http://www.caraudiodirect.co.uk/deadening/