I know this is a very old thread, but my son and I just ran 16 AWG speaker wires to the doors and it was fairly easy. We did not go through the molex. We did it the way KmanZ suggested. You'll want a helper.

1. Pop out the grommet on the car body below the molex.
2. My son fished the wire from the inside of the car while I shined my headlight on the hole on the outside. He was able to just use a small flat head screwdriver to push the tip of the wire where it poked out of the hole a tiny bit, and I grabbed the end with my long needle nose pliers.
3. Carefully pull 18-24" of wire through the opening.
4. Make sure to put a new grommet with a hole in the middle onto the wires before you do the next steps. We used new ones from a kit I have, but you could easily cut a slit or hole in the center of the old grommet.
5. Wrap the wires tightly and neatly with good electrical tape, starting about 6-8" back from the end that will go into the door. Wrap maybe 8-10" of length.
6. To then get the wires into the door, we heated up a pick with a torch, and poked/melted a small hole through the bottom of the rubber where the wire harness goes into the door, doing it from inside the door out. You'll see there is a fairly good sized flat area on the rubber below where the other wires come in. Let the rubber cool for a minute before the next step.
7. Spray/apply some silicone or other lubricant onto the taped part of the wires and the 8" or so that will go through the hole in the rubber into the door, and then push the wires through the rubber, making sure some of the taped part comes through the rubber. We used a small pair of long tip needle nose pliers to grab the end from inside the door.
8. Carefully pull enough wire through so you'll have enough slack to wire your new speaker.
9. Fiddle the grommet back into the hole of the car body.
10. Carefully pull the extra wire back through into the inside of the car.

This was much easier and less risky than going through the molex. The black electrical tape protects the wires and they actually naturally lay flat against the rubber tube between the car body and the door. You can add a bit of sealant where the wires go through the grommet and where they go through the rubber into the door, if desired.

We had both seats out and also removed the plastic dashboard piece under the steering wheel on the driver's side. The driver's side was a little tougher to fish the wire through. Both side were done in less than an hour. Hope this detail helps someone else.