No, I've never paid to have a transmission rebuilt, so I can not suggest a good place to do so.

When my AOD went south a few months back, it was cheaper to buy a slightly used one and swap it in, than rebuild the old one. However, Ive kept the old tranny, and later when I have the finances and time, will rebuild it, upgrading the valve body, overdrive band, etc. So to answer your question, yes, you can rebuild a transmission to be better than before.

Now, if your looking for a source of parts to beef up an Auto tranny, checking out Art Carr, and Level 10 performance would be a good start.