I can try:
When switching to taller gears, the rotational "slop" in the front driveshaft may increase due to the smaller driveshaft gear (more backlash). Since the front driveshaft is not loaded (since it is not typically in 4WD at highway speeds), the front driveshaft rotates about in the slop (slapping back and forth) when your chugging along at highway speeds and could be causing high vibrations of the drivetrain.
Has anyone or can anyone with the issue try to use 4WD at the problematic speed to see if it goes away? Maybe even use a touch of e-brake to load up the front driveshaft if the issue does still appear?
I have a stock 4 cyl TJ with stock sized tires (multiple sets) with harmonic vibrations similar to many described in this thread although not too severe. Also, there is no harmonic balancer on the transfer case output like the 6 cyl's were built with. And since there's no lift kit, no oversize tires, and no suspension mods, it takes a lot of variables out of the equation. Everything between the bumpers is as close to new as you can get it. What I haven't extensively replaced, I've measured runout on the rest. The wheels, axles, driveshafts, rotors, drums are all true.
Some of the things I've done with no effect on the harmonic vibration issue;
- new engine mounts, new trans mount twice - one stock OEM, one jobber (stiffer)
- removed the front D/S, carrier, and front shafts. Just the stub axles through the front hubs.
- 3 sets of tires, 2 sets of wheels, multiple tire re-balances
- rebuilt both driveshafts all Spicer parts, then had them re-balanced by a driveline shop
- shimmed the trans mount up 1/2", then removed it. Dropped the skid 3/4".
- body mounts, Centric drums and rotors, new shocks.
- new transmission, rebuilt the transfer case, new flywheel, clutch, harmonic balancer front.
You may be on to something redirecting focus on to the axle gears.