There's a number of reasons why your sub wouldn't work. Does your TJ have the factory radio or is it aftermarket? When you took apart your center console to change the speaker did you see the amp on the side of the sub enclosure? Did it look burnt, blackened, smell funny, etc.? How did the connector look that runs underneath the cup holders? That looked easily broken when I was upgrading mine.
Speaking of upgrading, this would be the perfect time to upgrade your sub setup instead of fixing the factory one. I used a kicker 6.5" sub and an amp I had laying around. Gives you more bass and replaces that crappy paper cone factory sub that is prone to breaking anyway.