1. I usually just put it in a new directory, just in case the new version is less stable; take the .txt file of my saved game over to the next one if I feel the need. You should wait for better input, though, as I'm not sure of your needs. Are you compiling the program yourself, or anything like that?
2. Talk to people; mostly, it's a matter of taking what they say on faith. For instance, if they say they have a Treasure Map, buy it. If they say they need help with something, help them. Once you've found the eventual object of this odd task, whatever it may be, scan over it with science or mysticism. If that doesn't offer you much info on the item, go back to the person who gave you the mission; then head back to the temple and report to the person who gave you the broader task of finding the artifact.
It's a little odd, but I've always loved Hwang-Sa missions.

3. If so, I've never found out how.
4. Yeah, I've actually fished out damning evidence from a file cabinet which had burnt entirely down, while the tile was on fire. Very funny.