Vibration while decelerating, gear chatter too!

Hi All,

Tonight while on my way home I noticed an odd noise while decelerating on the highway, it was a low frequency noise from the rear of the truck. I was decelerating from 75 to 60 or so. The noise carried throughout the transition.
When I got off the highway, I again noticed a vibration or chatter while in gear (doesn't matter which gear) and decelerating. If I push the clutch pedal in and apply brakes (in a non-emergency pressure) I get some gear chatter as well.
This is a 2010, 2.7 Manual with about 94k miles on it. This issue just popped up this afternoon with no previous vibration/chatter noises or feel.
When accelerating from a stop, I feel a slight slip of the clutch but nothing I would consider to be serious at this point. I tried decelerating in 4x4 and the same issue occurs and the 4x4 disengages with no issue.
Toyota at one point replaced the throw-out bearing due to the factory installing an over-sized bearing. The bearing would chatter while vehicle was parked and in neutral. The vibration/chatter issue was not present before or after that repair until now, and that repair may have been 2 years ago.

So I'm a bit at a loss here cause there are a few different symptoms and things going on at once. I almost feel it could be the clutch not releasing all the way. It almost feels like when the ABS kicks in on a slide but without the pedal feel and not as prominent. What concerns me is the gear chatter which makes me think it might be the transfer case or the front differential. We have some pretty nasty, unavoidable potholes since winter and I'm hoping that nothing was knocked silly or out of alignment in respect to another part.

Any ideas on this?
I plan on setting up an appointment with the dealer to diag the issue, but thought I would throw this issue out there to see if there were thoughts or if anyone had similar issues. From what I found on here it was torque converter issues, which doesn't apply.

Thanks for the help and insight, appreciate your thoughts.
Cheers!