I just updated the download. Here's a list of the changes from coolest to most banal:

-When you lose a boss fight, you're now given the option to retry (with a complete restore). This doesn't work on some special boss fights, such as the arena battles.
-I've added a second battle theme that plays after a certain point in the story. If you're past that point and you update the file, the battle theme will change to the new one after a boss battle. If you've beaten the game, you can change it either through the fourth fight in an arena or by fighting one of the boss battles again through Mort.
-The boulder puzzle should no longer glitch out and it's also slightly easier, but I haven't tested it on a really old computer. My computer is pretty crappy though, so I think it should function well across the board.
-The lights-out puzzle is a bit easier.
-I've added a staircase in the nested flame puzzle in God's Temple so you don't have to backtrack as far if you mess up.
-I've changed a part of the ending dialogue--nothing worth beating the game over again, but it should make the ending a bit stronger.
-Some minor npc dialogue has been changed in Attis.
-A few annoyance glitches that you may or may not have run into have been fixed.