I had almost exactly the same problem on my '96 SR5, with the 5-spd R150F manual trans. I had a helluva vibration between 65-75 mph, which returned as an ominous high-speed "buzzing" at speeds over 80.
After reading BigFishAllDay's EXCELLENT write-up on removal of front and rear driveshafts to access/replace t-case output shaft oil seals (found here:
http://www.toyota-4runner.org/3rd-gen-t4rs/101650-replacing-transfer-case-output-shaft-oil-seals-how-diyers.html), I unbolted the front of the rear drive shaft and moved it aside. I then discovered the culprit - the 30mm staked nut holding the rear companion flange (where the rear driveshaft bolts to, just ahead of the DC joint) onto the end of the t-case rear output shaft had simply come loose. Not loose enough to freely unscrew, but loose enough to allow the splines to separate every so slightly, allowing the companion flange to wiggle laterally about 3/16" in any direction. Miraculously the seals weren't leaking, nor were the DC spiders loose in any way. Just that damned nut.
So after yanking out the companion flange per BFAD's write-up, I cleaned up the splines and checked the outer surface of the spline shaft (it was still smooth as a baby's butt after a mere 351,000 miles) then re-installed with a new 30mm stake-nut, which I proceeded to stake the HELL out of this time, and torqued it to 87 ft-lbs, per BFAD again.
Got the rear drive shaft mated back up to the companion flange studs, making sure that the match-marks I made prior to disassembly were lined up, and torqued those nuts down to 54 ft-lbs (per BFAD). Had to use new grease pumped by my buddy Geoff into the zerk on the rear drive shaft yoke to push the drive shaft forward to mate the DC flange to the t-case companion flange, which worked like a charm. Greased the DC zerks, then took her out for a drive and discovered that approximately 98.3% of the vibration had been eliminated. I chalked the remaining vibration up to the typical 3rd Gen dump-truck ride quality LOL
I didn't bother taking any photos, as they are pretty well detailed in BFAD's write-up. But I hope that this is helpful to anyone experiencing the same sort of issue! Cheers all! :hatsoff: