My LJ has the same vibes from the rear. I have a brand new SYE, fully rebuilt/shortened/balance ZJ front driveshaft. Driveshaft and rear pinion angles match at 15 degrees. The vibes started with the 4.88 gears. Back then I was running the stock skid and stock rear driveshaft, once I did the tummy tuck the vibes were a loud worse and louder so I quickly did the SYE and new driveshaft. It's better than it was without the SYE, but starting at 68mph or so I have a pulsing vibration.
04 Rubicon, 5.5" RE LA with Tri-link, 35" KM2, 4.88's