E6 - E6 was created for 3.5 D&D so some of the rules are outdated and since no one has completed an E6 update specifically for Pathfinder we will decide on any discrepancies on a case-by-case basis.
Critical Fumble/Hits: I own the Pathfinder GameMastery Critical Hit and Critical Fumble decks, and will be using them in game. Fumbles use implementation option #1 (if you roll a natural 1, you follow it with a confirmation roll at your highest attack bonus, if that misses, you will receive a random yet appropriate effect from the deck). Confirmed Critical Hits replace 1x of your critical multiplier with a random card. Regular rules for stacking multiple multipliers apply.
Alignment & Honor: Alignment will be largely ignored. Remove all spells dealing specifically with alignment. Any class with an alignment restriction loses it. Paladins may worship any god, save 'evil' gods who have anti-paladins. 'Neutral' gods can have either paladins or anti-paladins.
Alignment will be replaced by Honor from the Dragon Empire Primer. A character's honor is represented by points, with a possible range of 0 to 100, a score of 0 represents someone who is untrustworthy and regarded as devious, and a score of 100 represents someone whose honorable deeds precede them. Honor is not a measurement of fame or goodwill so much as a gauge of loyalty, trustworthiness, and fairness. One could be a kindhearted-but flighty shogun with an Honor score of 0, or a cruel-but-stalwart monk with an honor score of 100. A character cannot have more than 100 honor points or fewer than 0.
Any abilities that deal with Alignment (Detect Evil, Smite Evil, etc) will be modified by honor.