They're only on eBay a few times a year. Your chances are much better on a Japanese auction site like Yahoo. It's rare, but not impossible to find. A complete in box version runs $80 on average. I was lucky and picked mine up for $25+ shipping.
How does it differ? You can check the Pre-release section on this site for details. It was released about 4 months before the retail version, so there's quite a few differences. I only recommend buying the Pre-release if you have a Pro Action Replay 2 or 3, you need codes to access the beta content. Otherwise you'll be limited to the demo areas (Factory Ruins, The Trial, Magus' Castle first section) which aren't very different from the final game.
