1. For places like the "fountain of ~" and strangers like the mage, when it is flipped up from a space that instructs you to draw, do you encounter it right away? Like when the fountain says put 4 of strength counters on this do you immediately take one so there would only be three. I know this may be a dumb question but just wanted to be clear on it.

You encounter them/visit them right away. Be wary that they have to be encountered in order by their encounter number.

2. What i the point of the gold and purple side of the fate counters? I have Dragons, dungeon, reaper expansions and it has not stated the difference betwen the two.

No difference. It's merely cosmetic.

3. With the good and evil weapons can an evil character aquire a "no evil character can have" weapon but instantly drop it. i would assume no unless something forced it into possession but then has to drop it immediately. Or can the cahracter under no circumstances have it?

A character may not pick up an object that he is restricted from taking(can't have)

Note that this is different from "cannot use". So, for instance, the Monk may pick up and carry Weapons and Armor as long as his alignment or carrying limit allows this, he just can't use them in battle.