I just went through what you are describing. As much as you may not want to hear it, you're likely going to need to pull out the transmission and send it out for work. Mine went to Gbox and ended up around the $3k mark (they will give you a range on costs, very understandable since they (Gbox) won't know what needs addressing until they are into it) with shipping both ways, I did the removal and replacement myself, really not that big of a deal if you have a bit of wrenching knowledge. While in there I'd suggest a new clutch package and IMS retrofit from LN Engineering. All totalled you are looking at $4K or more depending on what needs replaced inside the transmission. Good Luck.......Mark.
http://www.renntech.org/forums/index.php?/topic/32315-ims-rms-tranny-r-r-tips/