I have a 1998 Ford Ranger with 4 wheel drive and a manual 5 speed transmission. August of 2014 I had a throw out bearing go out and I took it to a local shop to have the throw out bearing replaced along with the clutch pressure plate and slave cylinder replaced. the fly wheel was machined and all was good for about 3 months when I started to have a hellacious chatter in the rear end as I let out on the clutch from a complete stop. I personally inspected the rear differential and had a my brother who is a mechanic verify that all was good in there. I also had the rear leaf springs inspected as instructed by the clutch shop where work was originally done. leaf springs were fine. The clutch shop said to drive it for a little while and see if it went away as according to them "Fords tend to have a chatter any way" went for about another month or so before I took it back and had the fly wheel replaced. 500 dollars a new fly wheel and another new clutch kit later (minus the slave cylinder) and about a week later and I have the same chatter in the rear end along with a tick that sounds like its coming from the transmission. I called back today and asked if the slave cylinder could be causing my problem and they said it was highly unlikely. It is not an exhaust hanger nor is it a heat shield. The chatter is strong enough to shake the whole truck. I don't abuse the truck by any means. I don't excessively ride the clutch either. I have exhausted almost all of my resources and am just trying to get to the bottom of this. Any help would be greatly appreciated.

 

I had kind of a similar problem several years ago. It was not as bad as you are describing but did so less severely. I took it to a powertrain company and they took the rear differential apart and could find nothing wrong with it. I continued to drive it and it continued to get slowly worse.

I eventually took it into a Ford dealership and they couldn't find the problem either but didn't give up. They put it on a dyno and just kept testing it to try to find where the problem was coming from. After several days the problem was found by a failure in the differential.

The carrier was cracked and was not easily visible when not under load. When the Ford dealership kept running it under load it finally broke all the way through. I ended up having to replace a lot more than the carrier because of all the damage.

I don't know if you have a similar problem but it is something to consider.