http://agtp.romhack.net/doukutsu.html <-- The patch is supposed to work for 1.0.0.6 and it's been updated and should work now. I haven't heard any _recent_ complaints about the patch not working.
Anyway, to get to your question. Pixel posted a while back on his BBS about the changes in the two versions of the games. Here it is, translated by Shih Tzu:
"There aren't any especially exciting changes, I'm afraid. After releasing version 1.0.0.5, I made some small fixes, but this was a long while back and I don't remember exactly what I did.
Changes I recall include:
* Reduced the CPU load.
* Expanded the 'Troubleshooting' section of the manual.
* Fixed the display of Naoku's picture in the manual.
* Added a sound effect for the Gravekeeper's attack.
* Added an effect for the Behemoth's charge.
* Fixed a bug in the Main Artery stage.
* Fixed a problem regarding processing issues on the title screen only."