I liked the comments so far.
Hey, Quickbeam, you might try totally rewriting the "favored enemy" part of this ranger-esque class you are designing. It sounds like this character is some kind of cult-breaker, or at least knows the tricks of clerics. Here are some suggestions for abilities to replace favored enemy (these ideas came from a secret police-type PrC for my Egyptian campaign)....Cheers!
Bonus to Spot/Sense Motive when confronted by a disguised cleric.
Studied Targets: Each time you would gain a new favored enemy, add a certian faith (or subclass) instead. Alternately, you have the ability to study a cleric for 3 days. After this time you get +2 attack, damage, AC, and saves vs. spells against that cleric. At first you may only have one studied target at a time, but when you would normally gain a new favored enemy, you may now get these bonuses against another specific cleric.
Weaken Priest: You can reduce the number of spells available to a cleric venerating an evil deity, or a deity considered “evil” by your faith. It takes a full action to use this power, and the cleric must be in close range (25 ft + 5 ft/2 levels). The affected cleric must make a (DC 12+WIS) will save or lose a number of spell levels equal to your character level. These spells come from whichever level(s) the Ranger chooses, though the affected cleric decides which spells are lost.