This is what you should be looking at now:

Now you're ready to start hacking! Get comfortable, this will take a while. You have a few options here. If you are very industrious, you can contact AMP (Tyco) who manufactures these connectors for Honda. I did and purchased the pin extraction tool and pins which will allow you to (non-destructively) remove the pins from the connector bodies (Multilock Series). You can then re-crimp new pins as needed. I'd suggest doing this if you can, if you ever go to remove the AFC to sell your car, you can simply cut the AFC off and re-pin your factory harness, truly setting it back to stock (without having to solder the factory wires back together).

First, the wiring diagrams. Use the first to determine which one you need for your car, then look up and print out the wiring chart:

  

This shows you exactly what wires you need to cut. Note that these diagrams are looking into the back of the connector where the wires are coming out.

Now, for those of you that are industrious, here's how to remove the pins. First, you need to "unlock" the pins by pushing up on the white plastic retainer. Pushing up from the bottom of the connector, you can unlock this piece "upwards" with a regular flathead screwdriver.

Once this piece is snapped "up" (about 1/16") you can then use the extractor tool or a small flathead screwdriver to release the pins:

You'll see a small slot by the connector pin "hole" where you insert the tool and then gently pry up while pulling the wire out from the back. This is a very delicate system. It does not take much force at all to remove these pins. You'll know when you have it right, as the pin and wire will slide right out. If there is any resistance, do not force it! You haven't unlatched the pin yet. With some practice it's not that bad.

For the rest of you, you will need to cut the factory wires. Try to leave as much slack as possible on both sides of the wire, you'll need room to work as well as make the connections. You may need to untape some of the factory wiring to get a little more slack. Pick a wire and start. Be sure (very sure) you have the right wire before you cut. I won't cover color codes here as they vary from model to model. Follow the A'pexi chart for your specific model.

For "parasitic" connections where you just need to monitor a signal, I suggest you still cut the factor wire, then splice the 3 together. Not only is stripping insulation off a wire (without cutting it) difficult, you usually end up cutting some of the strands anyhow. I suggest you cut the wire, strip both ends, then solder them back together with the sense wire from the AFC soldered on top. For intercepted signals, simply cut the wire, strip both ends, then solder to the new wires on the AFC. Be sure to solder and heat shrink all connections!!!

It's important that you use the power and ground wires going to the ECU. Do not pick another ground point or run power from another source. This is important not only for proper operation but also for accurate operation. Any change in potential in the supply voltage or ground may result in different detected/reported voltages by/from the AFC to the ECU. As an electronics engineer I don't put much stock in the AFC's requirement of one ground wire being closer to the ECU than another, but I followed their recommendation nonetheless.

Reinstall the footrest as it came out, being careful to not pinch any wires when you put it back in place. Tighten the nuts down, then reassemble all the trim you took out. Now is a good time, too, to route the AFC cable where you need it (in my case to the dash).

Continue on with Programming your Air/Fuel Controller.