Step 1: Remove Door Skin
A simple google search will be able to provide more detail, but it's pretty easy. There is only one screw (Phillips) that you need to remove, it's in the door grab handle (not the release handle). everything else pops out with a trim removal tool (don't use a regular screwdriver unless you want deep scratches all over in your plastic and paint).
Step 2: Remove Factory Speaker
Just three screws hold the speaker bracket to the door. Another three hold the speaker onto the bracket. The speaker might be stuck to the bracket with the foam stuff, just rip it off and throw that speaker away. Make sure to keep as much of the speaker wires as you can (a soldering iron might be helpful here, but I just cut it).
Step 3: Modify Speaker Bracket
My 6.5 Kicker speakers were too deep and a little wider than the factory speakers, so I had to cut away much of the old bracket to fit. First, I completely cut off at the cone thing, not sure why it's there, but you definitely don't need it. Then, I used my dremel with the sanding bit to grind the edges of the bracket to a roughly 45 degree angle, finishing with some 220 grit sandpaper just to even things out a little bit.
Step 4: Prepare Speaker Cables
Add female disconnects to the old speaker wires. It doesn't matter which wire is positive/negative, but negative is the wire with the stripe.
Step 5: Prepare Bracket
Because it's not going to be a perfect fit, and the screw holes probably won't line up, you'll need a good way to attach the new speaks to the bracket. I used some vinyl weather stripping and glued it to the 45 degree surface. This provides a near perfect fit because the vinyl is flexible enough to accommodate the surface of the new speaker.
Step 6: Mount New Speaker
I then just took some more super glue and put it pretty liberally along the inner top edge of the vinyl strip. Make sure to get the most possible surface area of the new speaker in contact with the weather stripping.
Step 7: Install
Connect your terminals to the new speaker (or if you're using an amp, do whatever you need to do for that). This is an excellent opportunity to add some sound deadening to your door, while the skin is off. I had a lot of luck with Frost King self-adhesive duct insulation (I've heard a of bad things about peel-n-seal). Rip the plastic off the door, apply frost King, and cut out holes for everything. I also used some 5/16" tube and stuck it in the weather stripping around the door to cut down on wind noise.
The new speaker should fit perfectly. Take some pics and let me know how it came out!