Small world Trev!!! I think the JLT is fine, but those headers will screw you. I don't know how stringent they are out here on those tests. You will fail the visual inspection with the LT's, depending on how smart the inspector is about Stangs, but you might (and I stress might) get away with the sniffer. Worse case scenario, you just keep your stock parts and switch back if necessary. You are looking at the exact same setup I'm shooting for. Good thing is that you won't have to worry about smog for a few years, but you should be more concerned about 5.0 and the noise you will be making.
IT WILL BE LOUD!!!!! 
My g/f says that my LM's sound like an airplane when I start it up in the garage and that's w/the stock H and headers. If you get on it, just watch who's around you, you know?
EDIT: I saw a couple of your other threads and just wanted to say good choice with the SCT. That JET thing is junk. The SCT is a piece of cake to use and takes like 5-10 min to tune the car. You won't have to worry about it running lean or anything like that. When modding your car, if it sounds too good to be true, it probably is. You can get one of the custom tunes or use the canned tunes until you get on a dyno. They will all work fine. I'm running on 91 and could tell a difference between that and 87. Good luck!!