Wow, awesome effort Serack.
I'd like to propose a revision to the "Morgan's animosity" in the Storm Front section. That's actually just a subset of possibly the single most important theme we've seen so far - Harry's different moral outlook than the Wouncil.
Harry, Eb, LtW and Rashid all believe in the possibility of rehabilitation for young wizards that have made one or two mistakes. This puts them directly in conflict with the views of other members of the Wouncil, notably the Merlin and Morgan. Harry goes even further than Eb and actually expresses the belief that the Wouncil has a responsibility to identify and educate young talent regarding the Laws of Magic before they have a chance to become warlocks.
This theme is introduced in SF with Harry's background and directly reoccurs in PG with the story of Molly and appears to be a major theme of GS (both Molly and the sorcerer's gang). It's also explored in Dead Beat with Harry's use of necromancy and in the characters of Cowl and Kumori. It's hinted that Maggie Sr. shared Harry's opinion that the Wouncil is shirking its responsibilities toward minor talents, which means this theme may reoccur when the mystery surrounding Harry's mother is explained (it's potentially what drove her to the Fae and/or Black Council). Harry's differences in opinion are what cause him to let Elaine go free in SK, it's partially responsibility for his involvement in WN, and it's what encourages him to help set up the Paranet so the minor talents can protect themselves where the Wouncil has failed. Finally, the answer as to whether Harry is right regarding the ability to rehabilitate emerging Warlocks is rooted in another core theme of the book - free will.
I'd write it like this:
Harry v. White Council- Rehabilitation of Warlocks
- White Council's responsibilities toward new and/or minor talents
- Morgan's animosity toward Harry
- Morality of necromancy