Well, you have a few options.
1 - Find out how to mate up LS sensor/dash signals with the Cobra's standard PCM. Might not be so hard if sensor output is the same on the LS. Or it might require custom hardware to get the sensor output at the proper levels. According to QuikLS, this is probably not possible without major doing.
2 - Use the original PCM and hack away at the code. Good luck here. Even the old EEV-IV systems in the late 80's/early 90's were pretty intensive. Ford tends to be assholish about releasing PCM code.
3 - Buy one from a company that specializes in custom PCM's.
4 - Just make your own cluster/swap in a Cobra cluster. This would also involve changing EVERYTHING else over to Cobra parts. Might be worth it. However, just swapping the engine harness over alone will be a 40-50 hour job. In spite of that, this is probably your best option.
5 - Roll your own. Most control over engine parameters, but if you don't know much about engine management, I'd stay away from this. You'd have to buy a relatively quick microcontroller/processor, high-speed multiplexor/demultiplexor, flash ROM, data bus, then build the PC Board to hold it all. Then you have to write the engine management code. It isn't impossible, but it sure is hard.