We have eliminated almost everything mentioned. The front axle shafts were removed and it was driven, that takes the entire front diff out of the picture. We even put a different set of control arms on the front for diagnostics. Vibe stayed there.
The vibe starts at 40 and is present whether coasting or under acceleration. There is a nice big slope coming to work and I shifted everything into neutral and it was still there. Some thoughts lean towards a bad bearing in the t-case. It's there in 4 hi up to 50 but not in 4 lo running up to 30 mph (did this as an experiment to rule out transmission issues) 4 lo at 1/2 speed in 2wd, vibes from transmission would show because of 2:1 gear ratio in t-case.
Any input on t-case?

 

Maybe try pulling the rear driveline and run it in 4 hi? Maybe your rear driveline lost a weight or is tweaked. Also look for runout on your rear axles, maybe you bent a flange.

 

I appreciate the input but please read my first post. Everything has been checked out. I was just basically wondering about the transfer case.

 

Did you check the ball joints? That wasn't mentioned in your first post.

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oops misread it, man I dont know. Sounds like you hit everything.

 

After what mod did it start vibrating?
Is the steering wheel vibrating or just a sound that sounds like vibrating?
Have someone follow you and look at tires and axles for wobble.
I put a go pro under mine looking at different components to find one of mine.

 

I know you checked everything, but it never hurts to check again. Sometimes you can't find the problem the first time or two. Good luck I hope you figure it out. I have a similar sounding vibe and part was my drag link and the ball joints are shot.

https://www.jk-forum.com/forums/jk-write-ups-39/write-up-diagnosing-death-wobble-fixing-non-dw-shimmies-wobbles-260145/

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Left me, an offroad shop and the entire local JK club scratching our heads too. I'm thinking maybe output bearing? The stealership said they couldn't work me in until July 9th! Even then not sure they won't flag me for the mods.

And on the ball joints...they are tight. No visible wear.

 

I see you have spent considerable hours trying different solutions to no avail.

Obviously your jeep worked fine when you bought it. And it worked fine with each subsequent mod up until some point.

Your problem is going to likely stem from whatever you changed. You said your alignment was spot on, so my initial thought of a defective control arm or bushing wouldn't work. Does your vibration worsen or improve when you hit rough spots on the rode while driving and experiencing the vibe problems?

You eliminated a defective tire, bad alignment, bad control arms, bad u-joints.

I've heard a drone/vibration could also stem from an unbalanced DL, but I see you've tested that too.

What about a bent output shaft on your T-case?
I don't know what you've done to your track bar/drag link set up, but that could be another area worth looking in to.

Sorry I don't have more ideas but it looks like you've worked through most of them!