Where is this noise coming from?

Pinion angle without a doubt causing a driveshaft vibration. Angle is going to depend on your setup. In other words in two piece driveshafts there is not a "set" angle. The angles from front to back have to cancel one another out. You can do a search on pinion angle on the internet and lots of visual explanations are out there in regards to what I am saying. The guys with the one piece don't have near as much to worry about. (Less joints = less calculation) I had the same problem with a Ranger both bagged and just plain dropped and did alot of research to solve the problem. By playing with the angles and matching to cancel one another out, the problem went away.

The problem if not fixed is that eventually that vibration can damage seals and bearings at your transmission tailshaft or rear axle yoke. Worse case, the seals will go while you are driving, you lose all your fluid, and toast a major component.