My biggest concern is that the full fighter BAB progession combined with the full cleric spell progression will cause problems for the campaign in terms of
1. Making it difficult for me to make sure the encounters are balanced.
2. Outshining the other characters in the party, particularly the Paladin, maybe the fighter.
I've tried looking at it from the prospective of the fighter class. A fighter would have to give up his bonus feats and his martial weapon proficiency. In exchange for this he would gain full cleric spell progression, a better will save, the ability to turn and the ability to spontaneously change those cleric spells into healing. From that prospective it seems does not seem so balanced to me.
To provide a concrete example a 12th level fighter would lose 7 bonus fighter feats and his martial weapons proficiency. This would provide 5 first, 4 second, 4 third, 3 fourth, 3 fifth and 2 sixth level spells (not including wisdom bonus), a plus 4 to his wisdom score, the ability to turn 3 times a day (not counting wisdom bonuses) and most likely at least proficiency with one martial weapon. That does not seem like a balanced trade.
A Pathfinder fighter would be giving up more abilities, things like armor mastery, bravery and weapons mastery.
The only thing that might keep this in check is keeping the ability scores relatively restricted. I plan on using the Pathfinder ability score buy with 20pts. With the Pathfinder the cost for higher scores ramps up faster than the standard point buy in 3.5 does.
Ysgarran.
p.s.
I really like putting the story first. It makes wonder why I am spending time with this in the first place.