Sorry to hear you didn't get a good one for the money. Sometimes a bargin isn't as good as it seems at the time. Hope things get better in the future.
I would go to a reliable Subaru dealer. They usually have rebuilt trannys for $2500 or so. Prices vary, so do some checking around. There are some 5 speed conversions as well. That is a little more money if you don't do it yourself. Do a search here, and you will find out quite a bit about them. There is also an article by Huck on how he converted his over to a 5 speed for $1,000. It is on the top of the page here, or in the "How-To Documents". Good luck.