The Main Quest Walkthru
(this is what you really came here for, wasn't it?)
The Main Quest is a series of many smaller quests that all lead to putting Lysandus to rest and reactivating the Numidium. These smaller quests do not have to be done at all (you can spend your whole career just wandering around the Bay), but you really should run through it at least once.
The Main Quest starts at Privateer's Hold (the dungeon where you start) and ends at the Mantellan Crux (where you find the Mantella which activates Numidium). Some of the quests will launch automatically when you reach a particular level. Others must be activated by talking to particular NPCs.
I have presented them here in (more or less) the sequence of the level you must be in order to activate them. It turns out that these pretty much split up into your two missions. You really can't start working on the Numidium until you are 5th level and you can finish off the mission to find the letter by 5th level.
If you turn down any of these quests when talking to an NPC, you can completely block yourself from the Main Quest, so exercise caution when talking to people in the three main castles.