At my tables, you get max hit points per hit die for determining your maximum hit points; if you level up in the middle of the dungeon, you add the die roll to your current hit point total (so the *die* still has some uses).

When I played 3.5, we ignored Favored Class as a ruleset. Now that we play Pathfinder, Favored Class bonuses are either specialized by race or the generic bonuses.

I have something called the 'open update policy' - that so long as you are using the most recent printed version of something - be it an ability, a class, a feat, weapon, etc., with Paizo/Dreamscarred Press taking precedent over 3.5 WotC sources. I'm also pretty lenient with third party material.