6x9 installation for contour

Did you ever think about just replacing the 6x8s with some aftermarket ones?  A whole lot less work, and if done properly will sound about the same as a pair of 6x9s.

Depending on how thick the aluminum is in the rear deck, you may be able to use a pair of tin snips to make your holes (or to widen existing holes if there are any).  If it's too thick for tin snips then a metal nibbler, airsaw, or dremel-type tool with a metal cutter would probably do the trick.

Also one thing you might want to keep in mind is that as there are not factory speakers already in this location, the rear deck cover might not give you enough space underneath it to mount a speaker, without it causing the hole cover to bulge up near the opening you cut.  I don't remember exactly what the deck looks like so I couldn't tell you for sure what you'll be facing, but I wouldn't be surprised if once you take the cover off you find yourself with hardly any room to top mount a speaker.  In that case, bottom mounting (from the underside of the deck) if really the only other good option in my opinion.

Yea that kicker amp will give you pretty good bass for the 8000.  Obviously the way to maximize the output is to get another 8000, then wire the two subs in parallel for the single 2 ohm load, and you'd have 200 going to each sub.  But in your case, 200 watts RMS to a single 12" thunder 8000 is still going to give you really good bass.

About the rear speakers:  just remember that to get that same kind of effect you're going to have to make sure the trunk is fairly airtight.  At the very least, make sure you put some foam around the edge of your cutouts before putting in the speaker.  Also try to plug up any other holes that you can find.  You don't have to go lining the entire trunk in a big foam seal, just try to fix the obvious holes as best as you can.

I don't know what year your vehicle is, but I saw some pictures of a 98 contour that had the jbl system in it, and the rear doors were insulated and sealed REALLY well  (photo w/ speaker in place, and w/ speaker removed)  I don't know if they only do that for the cars with the jbl systems or if all of them would be like that, but I just thought I'd throw that into the mix.