So I edited your post a bit, in exchange I'll answer what I can. Don't panic, nothing's wrong with it, I just wanted it clearer. And I haven't been honing my moderator skills in a long, long time...
4. I've never bothered to heal them, usually my only pet is the dog who is eaten pretty quickly after I stop needing help against hedgehogs... Attacking them with potion covered weapons works, but that also makes them angry. How about potion covered traps?
5. There is no way to clean them, but you can replace the stains with something else, like poison... Always keep your potions, wands and other brittle items in a box, and can your potions if possible. (In case you didn't know how to, dip the empty can into a bottle)
6. Strongbox is stronger, but it gets full with just a few wands and potions. There aren't many opponents that can actually break stuff inside boxes, so you're pretty safe with a small chest.
7. Izzy is a nightmare because he'll kill you by magic before you can even see him. I haven't had the fortune to meet him, or Sherry, or Golgor, or Xinroch... Yeah, I'm no power gamer. =P
8. The gods are handled in some thread here, don't remember which. If you can't find the altar you want, you can always try to polymorph one. Loricatus uses your int for the hardening, so you can't get valpurium stuff without the int to do so anyways.