I had my input shaft bearing retainer break on my 02 5-speed... it made a rattling noise like you described whenever the clutch pedal wasn't pressed in all the way. Eventually, the throwout bearing destroyed itself as well, and took the pressure plate with it; all of a sudden, I couldn't shift anymore. I realize that the input shaft bearing retainer and the output shaft bearing are two different things, but if the output shaft bearing checks out OK, I would look to the input shaft and clutch system next.
Dropping the transmission really isn't that hard of a job, you would just need jack stands, a good floor jack or two, and basic hand tools... I was pretty intimidated by it at first, but the various write-ups and threads about changing the clutch out helped me along quite a bit. I think I had the trans out of the Jeep within an hour; if you are somewhat mechanically inclined, I would recommend you save yourself the money and look into doing the work yourself.