Hello Destroying Angel, and you are absolutely right when you say the quest's clues are a bit confusing...they are!
Most players do the quests out of order and discover later that you missed something or have only a piece of the puzzle.
For me the most confusing part was knowing when the quests were over.
But let me tell you that following the clues, which are at times very vague, is the most difficult part in the quest storyline, as you will find out.
One thing I will tell you is...
DO NOT ENTER the Inner Core unless you have the best ship, weapons, and all the upgrades. Plus, you will need at least 6 hours to make it through to reach a safe dock.
Clarification of the quest clues would go a long way to stop any confusion.