when shifting from neutral to reverse a get a "clunk" type of sound that I beleive is coming from the tranny. No other issues, temps good, doesn't slip but I'd like to figure out what this is so I can fix it.

Any ideas?

Sounds like a u-joint to me.

OK here's some more info.

It seems to do it worse when the Jeep is parked facing uphill and then put into reverse. When I park it facing downhill and shift from neutral to revese it just slides right in.

I have just replaced the rear u-joints so I don't think its them. Could it be the front?