I recently bought a new transmission for my RS from Foster Auto Parts in Portland, Oregon. Their website is
http://www.fosterauto.com
The tranny I got ended up being bad. It had a problem shifting into 2nd gear. I let them know of the problem, they requested a quote from my mechanic to get it fixed. The quote was for a little more than what I paid for the tranny. Foster then refunded the full amount I paid for the tranny and let me keep the tranny (even though it is broken).
They were very easy to deal with, very nice and helpful and solved my problem in a very timely manner. I highly reccomend them for any "junkyard" parts you may need. Their website is pretty easy to find parts on and is up to date all the time. And if they don't have a part, they can find one for you in your home town. I actually found a transmission for my Hachi Roku through them in my town for $100.