Originally Posted by HCrum87hc
I was under the impression that removing the shaft on a pre 96 249 tcase wasn't recommended.
Well since you didn't take it back to the shop that put in the drive shaft I don't think you have much recourse here. The old shaft could have messed up the pinion or input shaft bearing or any number of things while it was wobbling at highway speeds. Not taking it back to the shop after you noticed a clunk and driving it several hundred miles wasn't the best idea.
It is bad for the VC to remove the front shaft but if you say that you can hear the clunk at low speeds then you could drive it a very short distance just to see if the noise goes away. If it does then you know it's the shaft or something it connects too. I wouldn't go on the highway or anything.
I would inspect the shafts u joints too while it's out.
A clunk can be anything. You just have to start ruling things out. Check everything in the front that rotates.