1. Yes village numbers will go up as you find them. You'll need to find village 4 to get access to quest 4. And village 3 to get access to all shop items. Numbering them will help you keep track much easier.
2. Max 3 stun means an enemy can only have 3 stuns applied to it. Combat effects last the rest of the fight, so if you were to hit the enemy with an electrified arrow, it would inflict 1 stun. On your next turn if you hit them again they'd have 2 stun. And again next turn for 3 stun. If you shoot them with an electrified arrow a 4th time, they don't get anymore STUN. It maxes at 3. Hard to summarize in the small space I had in the book, but hope this helps.
I tried to be very careful with my wording throughout the book, so if you don't see a rule that says you can do something, you probably can't.