I don't know of anyone making a harness compatable with the '03 Cobra motor. It will be a complete custom swap, with very little experienced knowledge from any where to help you. Probably the best approach is to start with a factory harness and computer and do what you need to get it to fit. With all the integrated systems it'll be hard to figure what you can leave out and what needs to be included, because by '03 the computer was getting feedback from things like emmission system valves and the A/C compressor as well as the theft deterent system. Leave something out or hook it up so the computer gets the wrong input and it won't run. You might be able to get an older 4V computer (like a '93-'94 Mark VIII) to run it with some custom programing. That might simplify the wiring some but it still won't be easy and there aren't many people capable of tapping into the ECM.
I see that you have it listed as a Ford Racing Cobra Crate Engine. I thought Ford Racing and SVT weren't offering the terminator engines as crate engines. Also, is it true that the 2003 motors are known to spit out spark plugs? Something about only having three threads per plug, but on 2004 engines they have 9 threads per plug?
I've done it and have helped many others do it as well. It's fairly straightforward these days. I use the factory ECU with a chip and some programming and sell a complete harness kit. You don't use an inch of the factory harness.
Drop me a line if you'd like to chat and I can run you through it.