1) +2 wells reset after you've been out of the zone 24+ hours. If you teleport into a zone you need to use +2 well(s) before reloading saved game in the zone. This is my experience w/ Free Haven and SC. (I vaguely remember that if you save and reload you have to allow 30 minutes to pass before +2 wells will work.) I tend to set up my heroes so that they have 15 Int, Per and End since those wells require travel day to reach. Also, if your permanent skill is 20+ the +5 wells won't add. If your skill is 25+ the +10 wells won't add. I get to +15/16 then +5 wells, then +10 wells, then +20 temple and then Black potions. Can get permanent base skills to 60+ this way. Means chasing skill development initially. Grayface patch fixes flag conflict between BS +5 int/per and KS +10 Magic Res wells.
2) I'd say random. I've slept in NS town and been fine most times but occasionally a monster will wander into town.
3) Stacking mainly applies to magic classes. The three artifacts that are "of x magics" can be stacked w/ rings "of x magic". When used w/ cast spells one item or artifact "of x magic" results in 150% result while stacked item and artifact result in 225% result. Generally spell strength and duration are both increased by these %. Know that "of power", "of protection" and "of the Gods" stack though A/R not required. Don't know about "of thievery" and many others. Interesting question.