Go to Crutchfield.com and enter all of your vehicle information. You can get installation instructions, as well as part and model numbers. 5 1/4 seems like factory, but 6 1/2 will probably fit with an adapter.
This is for an '05 with Bose and without nav:
http://www.crutchfield.com/S-n55qs7AEY9U/app/car/mycar.aspx
In my experience, mixing aftermarket with Bose is typically a bad idea. Bose amplifiers are matched to specific Bose speakers and tweeters (Bose tweeters are fairly unique). If you are going to replace the speakers, you should replace the amplifier or drive them directly from an aftermarket headunit.
The sub, the amplifier, and the sub enclosure are designed to work together as a system. Replacing the subwoofer and not replacing the amplifier isn't going to be worth the hassle, even if its possible.