Well...there is a flaw in your logic. First, it won't fit the LS...not without some serious modifications. That's the reason the 4.6 isn't in the car to begin with. You can make it fit...but that's the deal...you would have to do the work to shoe horn it in there. The exhaust system might be a real headache. Next, you will need to find a transmission that will work. Since the Cobra never came with an AT, the ECM isn't set up to control one. You would need a stand alone controller, an AT that isn't computer controlled, or switch to the T56. That's doable..but very spendy..and again you would be required to fabricate all the mounts and clutch system. You would need serious fuel system upgrades. The Terminator comes with dual fuel pumps. Believe me...there is a lot more than repinning involved to get the Cobra ECM to interface with the LS. They are two totally different systems and architecture. I really don't think it's possible to use the Cobra ECM (which is OBD II) and get all the functions of the LS...especially if the LS is running a CAN buss. I just don't see it...and I've done a LOT of this sort of thing. I really think you would be better off trying to control the Cobra engine with the LS ECM through flash tuning. Of course, you would probably lose some really good features of the Cobra engine that way such as both IAT temps, boost bypass, etc. But since the 03/04 Cobras do not use a knock sensor, and the LS does, maybe you could incorporate one as a failsafe since the LS ECM has that capability.
I own an 04 Cobra. I'm very intimate with it's features and what can be done to it. What you are saying can in fact be done since it's been done in the past. But the cost would be astronomical. If your buddy has a plan, I would love to see him post it up here.