Nope. the top rubber elbow where the tube meets the throttle body is different, ours is like a 90 degree bend theirs is 45 or something. I've wondered whether or not you could buy an 03/04 kit and just replace that part but, 1. i dont know where you would find that part, and 2. i dont know if the length of their tube is the same length as our tube.
Yes, the 99/01 Cobra and 03/04 Cobra JLT CAIs are the same EXCEPT FOR THE FOLLOWING:
Top rubber elbow that connects PVC pipe to throttle body
MAF adapter
Rubber piece that connects PVC pipe to MAF
EDIT: Some of the connectors might be different (like IAT sensor, vacum lines, etc.), but I am not positive about that one. Call Jay Tucker at JLT Performance and ask him.
You can go to http://intakehoses.com to find the 90 degree rubber elbow and the correct size rubber piece that connects the MAF to the PVC pipe.