1. Where does the game document which type of planetary bonuses are available on which types of planets?
It's not really publicly documented, you'd have to look in the game files.
2. Does the AI in this game know to move its capital?
Not really dependent on Forbidden Worlds, but I know it will if it loses its capital. Not sure if it moves for economic reasons.
This thread seems to suggest that pirates can jump from star to star? In my game the pirate was inconsequential because it was stranded.
That is correct, pirates can only attack in star systems with a pirate base.
4. What are the "occupied planets" found in Galaxy Forge?
Planet type used in the occupation victory, though they will not count for the victory condition if place manually in galaxy forge. They still have awesome stats though.