1. Yes, but some of them are too late for you now 
. There are some wells that boost your stats up to 15/16. Other wells give an extra boost but come with some disadvantages and(or conditions. The obelisk in Dragonsand gives some extra points 
if you survive the monsters. 2. Essence of xxx reduces some other stat. The potions to age is the one that increases SP with 100 (and maybe the one that increases HP). And the spell divine intervention also ages the caster.
3. To travel by stable (and ship?) to some cities you need first to get there (or was it to Silver Cove?) on foot. The way to get around that is to hire a gatemaster, she can get you to the cities with town wells without any previous travel.
4. It is not possible to enchant cheap items. Weapons that costs less than 250 gold are too cheap and to enchant weapons you need to be M in water. Other items have a higher limit, which I cannot recall at the moment (400 gp?), and for all stuff there is a risk of breaking it no matter how much it cost, which depend on how many skill points you have in water magic.
5. Yes, there is light and dark magic. You get it by joining the light and dark guilds and then buying the magic at the light and dark magic shops. Yes, it is worth it, especially the dark magic .
And my favourite link for MM6:
