Join Date: Dec 2001
Location: Belleville, Illinois
Thanked 22 Times in 17 Posts
There shouldn't be any break-in required of a pilot bearing or bushing. And usually the bellhousing mounts onto big, 3/8" dowel pins so shoulder bolts aren't necessary, but maybe they've changed that.
I could imagine a U-joint intermittently rubbing against something and making a noise like you describe that changes with engine speed and load, especially if everything isn't assembled properly and bolted together securely.
If it will misbehave without a load on the drive train, I would put it on jackstands under the axles and get underneath while it's making the noise. It should be easy to pin it down then. You need stands holding it up by the axles, not the frame, so that the drive shafts are in their normal orientation.