I am also interested to see where this project goes. I don't envy you the work you face though. You have a LOT of converting to do. However, I do have one comment. Keep in mind that you do not have to convert every cleric spell! You will actually need to decide what is important and what is not important from the cleric spell list. Some spells will outright not work well in this system, others are mediocre abilities at best.
On another note, you might want to look at making the domains more related to Disciplines. For example, using the crusader as an example, the cleric chooses 3 Domains (similar to the 3 Disciplines a crusader gains access to). Add a Universal Domain for core spells like Divinations that all clerics have, and these 4 domains are now the domains from which you can learn prayers, auras, etc. Then set up each domain similar to the disciplines in ToB.
For the domain itself, you could make the "Domain Power" into the equivalent of stances, thus they would gain 4 stances known (and maybe at 20th grant them stance mastery?). Instead of 1 spell per spell level gained as bonus prayers known, you are gaining access to the prayers related to the domains you know instead. This would create diversity among the clerics, even of the same deity (assuming the deity offers more than 3 domains).
Example Domain (1st level):
PROTECTION DOMAIN
Domain Stance: Sanctuary
…..1st Level
Deathwatch: Prayer - Reveals how near death subjects within 30 ft. are.
Endure Elements: - Prayer Exist comfortably in hot or cold environments.
Entropic Shield: Aura - Ranged attacks against you have 20% miss chance.
Hide from Undead: Prayer - Undead can’t perceive one subject/initiator level.
Protection from Chaos/Evil/Good/Law: Aura - +2 to AC and saves, counter mind control, hedge out elementals and outsiders.
Purify Food and Drink: Prayer - Purifies 1 cu. ft./initiator level of food or water.
Remove Fear: Blessing - Suppresses fear or gives +4 on saves against fear for one subject.
Resistance: Blessing - Subject gains +1 on saving throws.
Shield of Faith: Aura - Grants +2 or higher deflection bonus.
SANCTUARY (Stance)
Initiation Action: 1 swift action
Range: Personal
Target: You
Duration: Stance
Any opponent attempting to strike or otherwise directly attack you, even with a targeted spell, must attempt a Will save. If the save succeeds, the opponent can attack normally and is unaffected by the stance. If the save fails, the opponent can’t follow through with the attack, that part of its action is lost, and it can’t directly attack you for the duration of the encounter or until you switch stances. Those not attempting to attack you remain unaffected. This stance does not prevent you from being attacked or affected by area or effect spells. You cannot attack without breaking the stance but may use non-attack abilities or otherwise act.
Just a thought…