I'm a lot fuzzy about the Mustang harness, but most of that sounds familier. I installed a 98 GT engine into a 95 Crown Vic, many years ago.
As just recommended, I agree greatly that you should install the entire engine, trans, and PCM harnesses. The wiring that I believe you are talking about going into the dash are for the instrument cluster basically. You will be needing to tap into the start circuit and ignition wiring from the Mustang. I hope you are using the trans from the Explorer, trying to eliminate the CEL codes is not good.
Some of your difficulty will be placing the PCM, the Powertrain control module, not ECM. The harnesses aren't terribly long to get it far from the engine. Like my Crown Vic swap you will need to somewhat unwrap the underhood harness and reroute and rewrap the harness to fit your engine bay better. That harness will be able to replace the entire Mustang underhood harness, and all of the individual unique relays spread around the bay, and the green fuel pump relay under the seat. Take plenty of time doing that, make it fit well and look good also.
Use the entire Explorer front dress, hopefully it fits very well. The height might be a little different, and the AC lines should need some fabricating. I've got a Mark VII that I've thought of doing that to instead of rebuilding it as is.
The three ignition wire colors that I recall are Red/blue for the start ignition circuit, Red/green for the run ignition, and White/red for the trans circuit for park/starting.
You should not tap into the engine harness at all. The wires that you should need will all be in the engine bay harness at the three big square firewall connectors. Mount that big power distribution box and work on finding the wiring matches between those small Mustang bay connectors, and the three Explorer connectors.
I don't know if the wiring diagrams available on DVD's will cover all of the circuits that you need, that's where I would start. I have a cheap set which I bought many years ago. Mine are difficult to identify circuits in the pictures/diagrams. There may be much better manuals available. Mine shows basically all wiring, but everything is referenced to connector #'s, not actual circuits. More specifically each circuit is numbered, and wires are all labeled by circuit #'s, colors, and the connectors which they go to.
The hard part is identifying the circuit numbers. See what kind of wiring diagrams are available through eBay and internet searches(Mustang DVD manuals). Good luck,