I just went though this entire process on my 04 this past weekend. In a matter of about 4 months, 3 of the 4 main speakers died on me. I ended up with just the tweeters in the front, and one speaker in the back. I replaced all 4 with a set of JBL GTO629's and the harnesses. Sounds great now!
Some suggestions for you:
If the speakers you purchased only come with the plastic trim rings shown, the trim rings probably won't fit. However, you should be able to drill out the mounting holes on the speakers themselves and reuse the stock phillips self tapping screws to mount them in the stock housings.
Take care when removing the window switch housings from the arm rests, but realize it will take a pretty decent amount of pressure to get them to "pop" out.
While you have the door panels off, it would be a good time to lube your window gaskets.
Finally, buy a pair for your back doors now. After you replace the fronts, you're going to want to do the backs!