As I have had trouble finding a decent case with a seperate accessory compartment that fits Jag-Stangs, I thought I would post this as I found a case that fits relatively well. You will have to put about 1/2 inch to an inch of padding on the butt to keep it from moving up and down, but otherwise it fits the neck and body lengthwise perfectly. They also have a built in tuner and some cool designs.
http://www.postalmonkey.com/