Yeah, if you are going to do a swap go ahead and buy the auto. If not you have to do some heavy thinking. It isn't that hard to do the swap to a 5-speed and if you can get the auto really cheap it's probably worth it. I know there are a few exceptions but most automatics haven't been beat on too bad either.
Once you find the tranny you are going to put in the rest of the parts aren't that expensive and there are plenty of installation pages on the internet.