Where abouts are you located?
There's a place in New Jersey called JDM Engine Depot that sells used JDM engines and transmissions for a good price. You can also find their store on ebay. I think an NA automatic was about $300? I know it' used and all but it's much cheaper than paying $3k to get yours rebuilt. They occasionally have 5 speeds as well. Local pickup would be good but they also ship freight.
Are you planning on replacing it yourself or having a shop do it?
There's also this website:
http://car-part.com/
You can search on there for parts near your location.