I have a 99 xj 5 speed and when im shifting there is a thud sound. sounds like it comes from the rear but unsure. Its the most noticeable from 1-2 shifts all the other gears not so much. Any input on this?

 

There are a lot of causes for this, the most common one is worn universal joints in the drive shaft itself. With the parking brake applied as tight as it goes, crawl under your Jeep and grab the drive shaft and start trying to move it. Any movement of the U joints in their caps is bad, though if they're original chances are that they should be replaced anyway. The rearmost (at differential pinion) usually goes first. You should also look into greasing the slip yoke on the back of the transfer case. It's hidden underneath a black rubber boot.

If you replace the u-joints and grease the slip yoke and still have the issues, the problem can be loose/broken leaf springs, shackles, shocks, or transmission & motor mounts.

 

Good post.