If you still have the rotoflex in the rear that's probably the problem. Look at rear driveshaft where it bolts to the differential yolk. If you have one you'll see what looks like a rubber donut sandwiched in between. It's probably cracking and this is causing your noise. Suggest you do some research and replace it with a regular u-joint driveshaft. I lifted my D1, rotoflexes don't last when they're lifted. Probably too much pressure on them and they're not designed to flex that much.
You can yank the rear driveshaft, put the cdl in 4 lock high then drive it. If there's no vibration then the rear driveshaft is probably the cause. If it doesn't go away you can put the rear back, then pull the front and see if it goes away.
Go here
http://www.discoweb.org/index.html scroll left down to rotoflex to u-joint conversion, has pictures and instructions.
If you decide to to this you have many options.
1. They have a kit for this at Atlantic British.
2. You can take the driveshaft to a driveshaft shop. They can weld on the proper flange, put in new u-joints and balance it.
3. You can have a new driveshaft built.
4. You can order the fancy ones from Tom Woods or Great Basin Rovers.
5. You can find a good used D2 rear driveshaft, you still need to change the flange on the differential though and put the spacer in.
6. You can put in a new rotoflex, but I wouldn't expect it to last very long.
