mine is doing something VERY similar. except i have anew clutch, TOB, pres plate, etc. pulled the tranny out and the pilot bearing was disintegrated. the noise going into reverse was from the transmission input shaft still spinning a little even when clutch was it ( bc the pilot bushing was locked to it ). your seems very similar. however. i replaced the pilot, noise mostly went away, but now its coming back some. driving me nuts!.
turn the jeep off. and try to start with it in Reverse. see if it makes the noise once in R, or only going into it