Reviving this from the dead!
I think I may have figured out the cause of the highway wobble that everyone is experiencing. I believe that the cause (in my case) is a bad transmission mount.
When I replaced the clutch, I noticed that my transmission mount was badly worn. So worn that the rubber bushing had completely separated from the bracket that attaches to the transmission itself. I meant to order a new one, but forgot to and said screw it I'll fix it later. (edit: the rubber is still there, just separated on one side, I'll post pictures when I get the new one) I figured the bolts would hold it in place long enough for me to order one and I'll get it replaced before my first camping trip in this thing.
Well, after heading out on a test drive after installing the clutch, I was terrified when my 4Runner felt SUPER sloppy. It felt like I was getting hit with 70 mph side winds. I initially thought suspension, low tire pressure, etc., etc. After checking tire pressure, and seeing what everyone has done already with little results and knowing that the previous owner had replaced many of the suspension components before I purchased it thought it had to be something else.
So I began to play around a little bit and tried to replicate the conditions under which the wobble occurred. After a little bit of driving, I noticed that the wobble happened after every time I shifted gears and was exaggerated at higher speeds. I also noticed that if I sped up during the wobble, it helped correct the problem a little but when I let up on the pedal the wobble got WAY worse to the point that I was hitting the brakes hard to not lose control on the freeway. This got me thinking of my bad mount and curious if the transmission was rocking on the mount. That transmission is heavy and would definitely cause a sway if that happened.
To test my theory I cruised at freeway speeds (70 mph here in Utah) until the wobble came back, I accelerated to gain control, let up on the pedal and sure enough the wobble got way worse. So I put the car in neutral without hitting the brakes and coasted for a bit. Sure enough, the wobble went away and as long as I was coasting in neutral, the wobble did not come back. I coasted for about 1/4 to 1/2 a mile to an exit without any trouble.
So, knowing the condition of my transmission mount and the results of my tests, I'm about 99% confident that my issue is because of a bad transmission mount. I've got one ordered and should be delivered by Wednesday. I'll install it and report back! Anyone else experiencing this issue, I recommend checking out the transmission mount. You'll need a floor jack to be able to hold the transmission in place as you drop the cross-member, but it's pretty simple to do.
I'd be interested to know the condition of the transmission mounts of everyone else experiencing this issue.