The only thing I can disagree with is Ether and Elixir. The cooldown on those should be set to about 2 mins, imo. Or else they can easily be spammed and those regenerating MP actions that CNJ and THM have would be rendered useless to somebody with stacks of Ether and Elixirs.

Everything else seems pretty good, imo. Hell, Personally I think (didn't read it all. not sure if it was mentioned) that Alchemist should get a job like the fighting and magic classes are. It should become a Chemist and assist in battle by throwing items out to allies to heal and buff them. Perhaps some of the skills can involve making an item on the spot (wouldn't take nearly as long as crafting) and throwing it to its target. Being a Chemist could also gives items enhanced effects, such as 50% more HP gets healed when throwing potions, 25% extra MP gets restored if you follow an Ether throw after a Potion throw (combo system).