Took the dealer a day or two to decide how to fix it, so I was waiting to post. Apparently, this is a common problem with the TJs that have the precat manifold, not the old style(atleast deffinatly rubis), so I thought I would post it here in case someone else is having the same problem. Everytime the front end dips down during hard braking or whatever, there was a nasty grind. Started out not too bad, but got worse. The exhaust manifold bolts and the downpipe flange bolts work themselves loose. Dont' know why, but it happends a lot apparently. When they get loose, you get like 2 inches of play in the exhaust, and the driveshaft U joint (the middle one) wacks the downpipe. Jeeps fix for me was new hardware, new flange, and new downpipe, but mine was REAL beat up from not finding the problem for a few thousand miles.
Might want to get some loctite on your downpipe and exhaust manifold bolts if you got the precat headers.