Glass based amputation troubles
I'm thinking this game I want to get some nice legs, so I get some glass and a god. Then I start walking on the glass until I lose a leg. I get a nice new parchment leg and then head into the dungeon. Inside I pray and it becomes hardened leather. I also find 2 iron boots (AV 7). I go back to town, and throw down 2 broken bottles. I remove the boot from my flesh leg, but not my leather one. No matter how much I walk on the glass, I dont take any damage! I expected my left (leather) leg to not get hurt but my right one to be cut off in short order. The only thing besides a bug I can think of is that my agility is around 20 or so.

This is a indeed minor bug. You have to remove your armor and cloak, too. It is logical that they protect the leg somewhat in combat (cloak fully, bodyarmor 50% of its AV), but not so against broken bottles. If you have already removed them, check that you're not levitating.