Did the vibration start before or after you did all the mentioned repairs?
Did you do anything to the Jeep, before the vibration started?
Have you tried jacking all 4 wheels up in the air & bring it up to vibration speed, also try it in 4x4? Look around for something strange? I'd put the jacks under the axles, so as not to flex the suspension.

Thoughts;
- Harmonic Balancer?
- Driveshaft(s) not balanced?
- Pull the rear driveshaft & see if the vibration disappears, just be sure to put a bag over the transfer case tail housing.

 

They sell something for this exact application. I refer to it as a "Torque stripe". It comes in different colors and I assume different strengths depending on your torque value. You squeeze a line of it over the 2 mating surfaces and let it dry for a good while. Then if there is substantial vibration or movement between the 2 surfaces, you will see the "paint" cracked. Here is the stuff.

https://www.durablesupply.com/dytaprtoma.html


I'm also dealing with a similar issue, but not so much vibration. It's more of a real loud hum that starts around 60mph and doesnt go away no matter how fast I go. It definitely comes from the front end, but I wanna say it might be a bearing or something. Like I said, no real vibration... maybe just a hair. It's just a loud hum. I'll probably check out all the stuff in your list and see if I can track mine down.
I'm 90% sure the front diff fluid was serviced within a year or so before I bought the XJ last August... original owner was a retired Air Force mechanic and he was very meticulous about taking care of that jeep...

 

Checked the flexplate to torque convertor bolts today. All tight but one bolt is different then other 3. 3 of them are 15mm one is 14mm. Is it possible it could unbalance driveline?

 

That's a very viable assumption. If you can find a bolt that matches the rest, go a head and swap it out. Having the smaller bolt head and not having the washer flange on it may be the difference of a few grams, but at 3000 RPMs, it may be the problem.
Are you ok with starting the vehicle and crawling underneath while its running to look at the flexplate? Maybe that could give some insight as well. Obviously keep it in Park, pull the e-brake to engage, and use chocks in front and behind a couple tires.... all in the name of safety.