New 4.56 gears and now noise and vibration

Hello, I am a new member but have been visiting this site for months learning about my TJ. This is an awesome forum. I have a 2004 X model with 4.0 and 5 speed manual. I plan to move up to 33" tires so I had it re-geared from 3.07 to 4.56 by a local offroad shop. The shop did 2 heat cycles on the gears prior to me picking up the vehicle to ensure the break-in process was done correctly. As I drove away I noticed a hum beginning at about 45mph that got progressively worse the faster I would go (seamed to come from rear diff). I kept the jeep below 55mph hoping things would smooth out. After about 20 miles I ran it up to 60mph and the sound was significantly louder and I could feel it through my seat and it was resonating inside the jeep. The noise would increase with speed but not really impacted by acceleration or pushing in the clutch. I pulled over and the rear diff was very hot to the touch. I sat for about 20 minutes to let it cool a then limped back to the shop using back roads keeping my speed below 45. Upon arrival they used an infrared thermometer and the rear diff was 185 degrees. They didnt seem too concerned but said they would look into it. The shop did mention they had an issue pressing on the pinion bearing. Apparently they had to order a second bearing as they were never able get the first one to fit. The shop is a Yukon certified installer and used Yukon gears. I am concerned because the cost of the regear was not cheap. Any insight or wisdom I can possibly share with the shop is greatly appreciated. Thank you.
With no change in noise while accelerating, de accelerating, or pushing the clutch in, and being solely speed dependent. It shouldn’t be the gears themselves unless they had a new guy and he set the backlash at an absolute zero. Does it sound kinda like those little electric kid jeeps driving around, or more like a front wheel bearing roar?
 
Update - Installer found one of the ujoints had a missing roller pin that had apparently fallen out during the re-gear. Replaced with a new u-joint but when I went to pick up the jeep the buzz is still there. I asked about using gear marking compound to confirm the ring and pinion contact patterns look good but was told since the gears are mostly broken in the process would not tell us anything. I have also asked about checking the backlash to confirm it is within tolerance and the installer seems to be against doing either of these tests and is pointing toward possible driveshaft alignment as the vibration source. The gears have approximately 300 miles on them now. Can someone comment on why gear patterns and backlash are no longer relevant? My research seems to indicate both test are very important to help diagnose a noisy differential (even after break-in and well beyond). Any help is appreciated.
 
Update - Installer found one of the ujoints had a missing roller pin that had apparently fallen out during the re-gear. Replaced with a new u-joint but when I went to pick up the jeep the buzz is still there. I asked about using gear marking compound to confirm the ring and pinion contact patterns look good but was told since the gears are mostly broken in the process would not tell us anything. I have also asked about checking the backlash to confirm it is within tolerance and the installer seems to be against doing either of these tests and is pointing toward possible driveshaft alignment as the vibration source. The gears have approximately 300 miles on them now. Can someone comment on why gear patterns and backlash are no longer relevant? My research seems to indicate both test are very important to help diagnose a noisy differential (even after break-in and well beyond). Any help is appreciated.
That doesn’t make sense to me. I thought even an old gear set could be removed from one diff and set up in another, so it shouldn’t be unadvisable to not check the pattern and BL just bc the gears are broken in.
 
That doesn’t make sense to me. I thought even an old gear set could be removed from one diff and set up in another, so it shouldn’t be unadvisable to not check the pattern and BL just bc the gears are broken in.
You can move used gears over to another diff. None of my setters like to do it because they can't match the pattern that the gears were run at and the new pattern is always in a different place which makes things a bit wonky trying to figure out where to put them.
 
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Update - Installer found one of the ujoints had a missing roller pin that had apparently fallen out during the re-gear. Replaced with a new u-joint but when I went to pick up the jeep the buzz is still there. I asked about using gear marking compound to confirm the ring and pinion contact patterns look good but was told since the gears are mostly broken in the process would not tell us anything. I have also asked about checking the backlash to confirm it is within tolerance and the installer seems to be against doing either of these tests and is pointing toward possible driveshaft alignment as the vibration source. The gears have approximately 300 miles on them now. Can someone comment on why gear patterns and backlash are no longer relevant? My research seems to indicate both test are very important to help diagnose a noisy differential (even after break-in and well beyond). Any help is appreciated.
Stop asking them if they did the job correctly. You can't do it, you don't know how to do it and nothing is more irritating than someone who doesn't know shit trying to tell someone how to do their job.

You only have to say one thing. This isn't right, I don't know what is wrong but it shouldn't be like this, fix it.
 
With no change in noise while accelerating, de accelerating, or pushing the clutch in, and being solely speed dependent. It shouldn’t be the gears themselves unless they had a new guy and he set the backlash at an absolute zero. Does it sound kinda like those little electric kid jeeps driving around, or more like a front wheel bearing roar?
My money is on the driveshaft based on what is reported so far. That and the shop should be telling him that.
 
Update - Installer found one of the ujoints had a missing roller pin that had apparently fallen out during the re-gear. Replaced with a new u-joint but when I went to pick up the jeep the buzz is still there. I asked about using gear marking compound to confirm the ring and pinion contact patterns look good but was told since the gears are mostly broken in the process would not tell us anything. I have also asked about checking the backlash to confirm it is within tolerance and the installer seems to be against doing either of these tests and is pointing toward possible driveshaft alignment as the vibration source. The gears have approximately 300 miles on them now. Can someone comment on why gear patterns and backlash are no longer relevant? My research seems to indicate both test are very important to help diagnose a noisy differential (even after break-in and well beyond). Any help is appreciated.

Like me (based on your description), they probably don't think the noise sounds like gears. Being broken in doesn't mean the pattern or lash wouldn't be telling, but it does mean that it's too late to change anything to fix the pattern, so it's not worth pulling a cover just for that.

If you'll install Vibration Isolator Pro on your phone and run it, while the noise is good and strong, with the phone sitting flat on top of your cup holders, and post the screenshot along with what speed you were going at the time, that can help point to a driveshaft balance issue. In my experience those are more felt than heard.

Did they have any comment on the pinion bearing?

Also Blaine gives good advice. Nobody likes being told how to do their job by someone that doesn't do it. And they really don't like being challenged by information taken from a forum, because most forums aren't populated by knowledgeable folks like this one is. I usually play dumb and ask a lot of questions. It goes a lot better and I usually learn something.
 
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Also Blaine gives good advice. Nobody likes being told how to do their job by someone that doesn't do it. And they really don't like being challenged by information taken from a forum, because most forums aren't populated by knowledgeable folks like this one is. I usually play dumb and ask a lot of questions. It goes a lot better and I usually learn something.
A shop installed a big brake kit. The owner contacted me with a complaint that his rig now had a hard pull to the right under braking. He failed to mention that he did not do the install himself but had a shop do it. Many emails back and forth with me telling him what to check and him saying repeatedly that he had done all of it and the brake kit was the problem and I was wrong finally led to him revealing that a shop I know did the work and they fucked it up. I insisted that this shop that I know well did not fuck it up. Yes they did. Back and forth until I finally got fed up and told him fine, just bring it by and I'll fix it. But, if the shop didn't fuck it up, you're paying me for all my time. If they did fuck it up, its all on me.

Go to the right side, pull a tire, rotor is wobbly like a very large amount. Hey, look at this, there's the problem right there, unit bearing is shot. I show him the rotor moves easily.

I looked it up on Google and You Tube, the rotor is supposed to wobble like that with the tire off.

Nope, not when you run wheel spacers. The wheel spacers act just like the tire being bolted up. Here, that will be 150 for a new unit bearing and 50 bucks for my time. Next time, don't argue with the folks that know what they are doing.
 
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I am no expert for sure. Now that I have much more seat time with the new gears I want to update my symptoms. I can feel the the vibration most of the time above 45 however at times it is mild below 55-60mph. The intensity is tied to vehicle speed however, acceleration and if you are going up an incline is impacting the intensity. Higher speed is where it is most noticeable and at 70 it can get intense at times but will decrease significantly by backing down a few mph. If I am accelerating or going up a incline it is more noticeable at a lower speed. I was going up a mild hill and the vibe was very noticeable at only 50 mph. I failed to mention that the vibe seems to be more noticeable as the diff gets hot. You cannot hold your hand on the diff and the shop owner has indicated temp is a concern as it appears to be on the upper end of what he considers acceptable (185 degrees). The symptom is not easy to explain and I am doing the best I can. I apologize if I am confusing everyone. I plan to let the shop do their job.
 
A shop installed a big brake kit. The owner contacted me with a complaint that his rig now had a hard pull to the right under braking. He failed to mention that he did not do the install himself but had a shop do it. Many emails back and forth with me telling him what to check and him saying repeatedly that he had done all of it and the brake kit was the problem and I was wrong finally led to him revealing that a shop I know did the work and they fucked it up. I insisted that this shop that I know well did not fuck it up. Yes they did. Back and forth until I finally got fed up and told him fine, just bring it by and I'll fix it. But, if the shop didn't fuck it up, you're paying me for all my time. If they did fuck it up, its all on me.

Go to the right side, pull a tire, rotor is wobbly like a very large amount. Hey, look at this, there's the problem right there, unit bearing is shot. I show him the rotor moves easily.

I looked it up on Google and You Tube, the rotor is supposed to wobble like that with the tire off.

Nope, not when you run wheel spacers. The wheel spacers act just like the tire being bolted up. Here, that will be 150 for a new unit bearing and 50 bucks for my time. Next time, don't argue with the folks that know what they are doing.

The complete lack of critical thinking skills in that process. He read the rotor would be loose but didn't notice that the entire hub flange and the lugs were wobbling with it and didn't even begin to process WHY the rotor wouldn't be tight. Also makes me wonder if the shop told him he needed a unit bearing and he declined the repair.

It would have taken everything in me not to also charge him for the time spent emailing back and forth with him.
 
The complete lack of critical thinking skills in that process. He read the rotor would be loose but didn't notice that the entire hub flange and the lugs were wobbling with it and didn't even begin to process WHY the rotor wouldn't be tight. Also makes me wonder if the shop told him he needed a unit bearing and he declined the repair.
No, that shop would not have let him leave with a bad unit bearing or if he insisted, they would not have installed the brake kit. I was more irritated that he worked me for days trying to get me to throw the shop under the bus by not telling me who did the work. I gave him a list of things I needed him to check and he kept replying almost immediately that each and every item was done and checked.
It would have taken everything in me not to also charge him for the time spent emailing back and forth with him.
I was much nicer about it that I really wanted to be.
 
You can't hold your hand on a differential even when it's working perfectly well and at its normal operating temperature.
Or put another way, how many times did you check the temp of the diff with your hand before you got it re-geared? That's right, not once so you have no idea how hot it can be in order to be able to hold your hand on it.
 
Well I guess I am one of the few who have checked their diff temp by hand. When I changed my rear pinion seal I noticed it was very warm. It was hot enough that I drove and checked it again and topped off my fluid just to ensure it was full. However, it was not as hot as my diff gets now. I also understand the break-in process and possibly the new gear ratio could create some additional heat. Sounds like the temp is normal so thanks again for input.