1. What's with Dr. John - who is he really? What's with all the blood and stuff in his room?
Just a guy who happens to be the right-hand man of the main villain, but with a more physical presence. Blood and stuff, you mean at his altar in the hounfour? That's just ritualistic offerings.
2. What's with the Morgue? What the heck is going on in there...
Morgue? Oh, you mean that room in the hounfour? It's where they harvest human hearts, needed to open the shrine in the main room.
3. Who is that guy who just stands outside the bookshop staring? (creepy)
Sughly explained already. Just an observer of the voodoo cult.
4. How was Wolfgang able to rip out his own heart and place it there?
No idea, sheer force of will I guess.
5. What was the fate of Gabriel's father and grandfather?
Since they turned their backs to the Shattenjäger life, they both died young, I believe in accidents (bad karma, probably).
6. Why is Grace so cool?
She's voiced by Leah Remini, for one thing, but as a character she just knows the right buttons to push.