I went through what you are describing earlier this year. I also did the IMS retrofit while in there along with replacing the clutch and RMS. If you take your time and follow the Bentley Manual it is not too tough of a job. Rebuild through Gbox will run $2400 to $3400 depending on what needs done (for an "S" 6 speed, yours may be less) plus shipping.
http://www.renntech.org/forums/index.php?/topic/32315-ims-rms-tranny-r-r-tips/?