I'm actually planning to use Academy of Secrets as part of my replacement for History of Ashes (the whole cowboys & Indians theme just doesn't do it for me). In my alternate plot, the party first has to rescue Thousand Bones from Deathhead Vault, where he's been imprisoned as an "enemy of the people". They're hoping he can tell them what was kept hidden by the Shoanti in the ancient mastaba. Unfortunately, he can't, but he knows a Shoanti shaman who possibly can. The bad news is, he's been captured by the Knights of the Nail, and is being held prisoner in Citadel Vraid.
The party journeys to the Citadel and negotiates with Lictor DeVries for the Shoanti's release (I hope to convince them that assaulting the Hellknights' stronghold is a Bad Idea). He agrees on the condition that they retrieve an item for him - something kept in the Hall of Warding in the Acadamae.
This takes us into Academy of Secrets. I'm going to dispense with the whole Breaching Festival thing. Instead they have to steal the key from the headmaster's quarters (yikes!) then use it to get into Belzeragna. The item DeVries wants is his contract with his hellish master, kept by the Contract Devil.
Once they've freed the shaman, he'll lead them into the Cinderlands to commune with the ancestor spirits (no Respect Points shtuff) to get the skinny on Kazavon and Serithial.