Has the gear lube ever been changed in the manual trans? i have had that same noise in previous cars and trucks with manual trans. i switched to synthetic and literally drove for 50 thousand more miles before i sold it. sounds like it is the input shaft bearing. somebody correct me if i am wrong, but if i remember correctly the nv 3550 (your transmission) does make more noises than usual due to its truck design origins from its bigger siblings in 3/4 ton trucks and up.
now i know the owners manual states that the manual gear lube just needs to be checked and not changed(at least in my liberties 6 speed manual). but i always change the gear oil out at 15 to 20k to prevent moisture from getting in and to prevent any noises from creeping in. it is cheap insurance.
it is hard to say without hearing the noise if it is at an acceptable level? good luck, mike
p.s. if you have the 7/ 70 warranty raise some heck at the dealer.
06 kj 3.7l, 6speed manual, np241 command track
91 yj 2.5l, ax-5, np 231 3 inck lift, 31'' mud rovers
12 kk 3.7L, 42rle, mp1522, d-30, 8.25.