Have an 88 Samurai with the stock 5 Speed Trans. Am experiencing gear noise (clatter if you will) mainly in 3rd and 4th gear. You can hear some in 2nd, but not as pronounced as 3rd and 4th. This thing is strictly a trail buggy, the only road it sees is those that take you from the trailer to the trail.

Some other facts... It does not matter what the Tcase is in, the noise is still prevalent. As a test, I put the T case in neutral, started running through the gears...

1st - Ok.
2nd - Some
3rd - Noise
4th - Noise
5th - Cannot shift into fifth anymore.

This has been going on since I bought this thing about a year or two ago. Thought is was the t-case, but when I put the 4:1 case in, the same conditions exist.

Any thoughts?

It sounds like a bearing in your transmission started to go and took your gears with it.  A friends 5 speed was like that, lost 3rd and 4th gear.  When we tore into it the gears were sharper then most kitchen knifes. 

I would look for a junkyard 5 speed you can rebuild, or buy a known good one from Hawk or one of the other aftermarket shops.