I haven't dug into the rear diff yet, so I assume that will be the next thing to do. It's been almost 2 years and 15K miles on the new gears with no resolution in the vibes, so I though I should summarize my re gear fiasco and write down to the best of my recollection the order of events. It's a long read so enter at your own risk.
"My re-gear fiasco
Feb, 2016 re-geared the rear axle to 4.56 gears and refreshed the Traclok with new Yukon clutches. Also changed the right rear axle bearing and seal due to the seal leaking a bit. Didn’t have time to re-gear the front, so drove it home in 2wd and immediately had vibrations above 45 mph. Next day removed the front drive shaft just to play it safe and vibrations went away. Drove it for a few weeks to break in the gears, then finally had time to do the front re gear. After re gearing the front and re-installing the drive shaft, the vibrations came back. Drove it for the next few weeks to break in the gears, keeping it below 45 mph to avoid the vibes. Thought that maybe my front drive shaft was the cause of the vibes, I ordered a brand new Adams drive shaft. Had planned trip to Moab in May, so after the 500 mile break in period, changed the gear oil and installed the new front drive shaft. Vibes were still present, but seemed a bit less severe. Decided to pull the front drive shaft again and drive to Moab with it out. Got to Moab, re-installed the front drive shaft for a week of off roading, then removed it for the drive home. 2000 miles round trip. The new gearing was great. The vibes, not so great. When I returned home, I took the jeep to an off road shop near by thinking maybe something was wrong with the front re gear. Noticed at that time the right front axle seal was leaking, so asked the shop to change the seals, and install a new Spicer yoke to upgrade to the stronger u-bolt style. The shop said the gears looked fine and replaced the seals and yoke. Vibes were still there just like before. Thinking that maybe the new front drive shaft I got wasn’t balanced good enough, I called Adams and they sent me a 2nd new front drive shaft. Installed it with no change in vibes. Went to a buddy’s house and swapped his wheel/tires for mine to rule out a wheel/tire issue. Vibes still there even with his known good wheels/tires from his jeep.Took the jeep back to the local off road shop to have them inspect the drivetrain. Shop noticed the rear drive shaft had some play in the slip yoke, so I figured this may have had something to do with the vibes. To verify, I pulled the rear drive shaft and went for a drive in 4hi. Vibes were almost gone. Only a very slight vibe. Decided to save up for a SYE and rebuild of the transfer case. Pulled the TC and took it to a local transmission shop I trust and had them refresh the TC with new bearings, seals, and chain as well as install of an Advanced Adaptor’s SYE. Re-installed the TC, took measurements for a new rear DC drive shaft and called up Adam’s drive shafts to order. Installed the new rear drive shaft, adjusted pinion angle and went for a drive. The vibes were there, but felt different. Above 45 mph I noticed a harmonic wave type of vibe. Still felt it in the seat and floor board. 65 mph and above the harmonic turned into a constant vibe. Tried adjusting the pinion angle at different angles from flat 0* to 1*, 1.5*, 2.0*, 3.0* with no change in vibes. Had my local mechanic check the motor mounts. They checked out good. Replaced the rear track bar with an adjustable one. The factory rear TB bushing didn’t look too good, so I figured it couldn’t hurt. Didn’t change the vibes. I inspected the trany mount and it seemed fine, but ordered a new one anyway. That is next on the list to change. Checked run out on both rear diff yoke and rear TC yoke, plus the new rear drive shaft. Runout was minimal. Called Adams and had them send me a 2nd new rear drive shaft just to rule it out as the problem. Installed 2nd drive shaft. No change. Vibes still there. While the rear driveshaft was out I took it for a drive in 4hi. Vibes almost gone. Only a very slight vibe at 65 mph. During this span of time I have also replaced the control arms with Metal Cloak arms. I had Currie lowers in the front, so when I bought new MC lowers, I put the Currie arms in the rear and the new MC’s up front. Put MC double adjustables in rear uppers.
It’s been almost 2 years and over 15,000 miles on the new gears with no resolution to date. "