Here is where I am hoping to end some confusion on which versions of things to use. This starts with Cleric Domains. Those listed as Pathfinder use the Pathfinder rule. Those listed as 3.5 use the 3.5 rule. Pretty Simple, right?

Air (Pathfinder)
Animal (Pathfinder)
Artifice (Pathfinder)
Community (Pathfinder)
Darkness (Pathfinder)
Death (Pathfinder)
Earth (Pathfinder)
Healing (Pathfinder)
Fire (Pathfinder)
Glory (Pathfinder)
Nobility (Pathfinder)
Plant (Pathfinder)
Sun (Pathfinder)
Water (Pathfinder)
Weather (Pathfinder)

Destruction (3.5)
Strength (3.5)
War (3.5)
Chaos (3.5)
Law (3.5)
Protection (3.5)
Knowledge (3.5)
Luck (3.5)
Travel (3.5)
Magic (3.5)
Evil (3.5)
Good (3.5)

Skills function pretty much the same. But there are some truncated options on the Pathfinder rules. If your 3.5 character class has a skill that gets combined with another in Pathfinder, you get the new Pathfinder skill as a class skill. The Truncated Skills are below.

Listen & Spot are now Perception
Open Lock & Disarm Trap are now Disable Device
Jump, Tumble, & Balance are now Acrobatics

When it comes to Skill Points, we're actually using Pathfinder's rules. So no x4 at level 1. No paying double for cross class skills. Instead, all skills are a single skillpoint. You get class + intelligence modifier skill points per level. You cap in ranks is your level, and for every class skill you have at least 1 rank in, you get an automatic +3 bonus.

ON FEATS: I know I like to keep things simple and this is one particular spot where it can get convoluted. So here goes.

1. Use my House Rules first.
2. Use Pathfinder.
3. If it is a combat feat like Improved Trip or Improved Bull Rush that uses Combat Maneuver checks, use the 3.5 version. Specialty attacks still cause damage.
4. If there are two versions of the same Feat, like Power Attack, use 3.5
5. If there are two versions of the same feat but it happens to be named something different, don't be a doofus. Take one or the other, not both.
6. If you really, really want it but Pathfinder says it doesn't exist, go with the 3.5 version.

There. Hopefully his will stem confusion.