Okay I have two issues going on currently I think I'm on the right track so far with my diagnosis but I'm just looking for any other options or thoughts from the guru's.

Issue #1) I have what I like to call a clutch chattering when the clutch is being engaged (going under load) it shake's the whole jeep, mostly in first gear or when down shifting from higher gears to lower gears. I think it has to due with the pilot bearing. I recently replaced the clutch, pressure plate and throw out bearing the pilot was the one part I didn't replace mostly because at the time I was under the impression most of my issues were the pressure plate. The flywheel looked really good and it's only had about 78k on it. The jeep did have this issue prior to the install and I've double checked the torque on all the bolts.
I have also replaced all the u-joints.

Issue #2) I'm thinking this could be a clutch master cylinder issue or slave issue. If I'm in heavy traffic or just on the clutch frequently I notice what seems to be a "clutch fade" (only term I can think of to call it) it seems like the clutch petal engagement and disengagement was reduced. Almost like I have an internal leak between the master cylinder or slave cylinder. The clutch fluid is full and I removed the boot on the slave and looked at is and it's dry. Maybe I got some air in the system somehow ? If I wait a few moments it goes back to normal though.

Sorry if any of this was confusing its kinda hard explaining things via text so I'm trying to explain it the best I can. Thanks for reading.

-Chris

Also I will be pulling the flywheel off and having it resurfaced when I change the pilot bearing.

 

#1: I had the same problem regarding the shaking of the jeep. You might look into replacing your transmission mount. Thats what I replaced and the shaking is 90% gone.

#2: Since you have no leak of fluid I would put my money on air in the system. Potentially it could be your clutch fluid becoming too hot causing the viscosity to drop and performance to decline. Maybe replace with DOT4 for higher boiling point.

 

^ I second the transmission mount. Also, make sure your transmission crossmember isn't split/cracked like mine was

 

Did you get flywhell resurefaced ?