First off, can they get flanking bonuses? If so, are the positions they need to be in the same but moved back a square?
Second, weapons that threaten 5 ft. around the character, also threaten squares that are diagonal in relation to the fighter, two squares diagonal from the fighter counts as 15 ft. of movement, so where does the reach fighter threaten diagonally if at all? One square away is 5 ft which is to close, and two squares in that direction is considered 15 ft. which is to far.
Third, if I am fighting a large a large creature and I am standing adjacent to it with a reach weapon, if the square I threaten is one which he is occupying, since he takes up a 10 ft. square, but he is still adjacent to me can I attack him without moving?
I don't know about flanking, but as far as the diagonal reach, it's finally been established that reach weapons are an exception to the diagonal movement rules: you DO threaten that square. It avoids certain absurd results.
First off, can they get flanking bonuses?
-Yes
If so, are the positions they need to be in the same but moved back a square?
-Basically. Attackers need to be on opposite sides - a line between 2 attackers must pass though opposite (non-adjacent) sides. Can be frustrating when on the corners because you can only flank from opposite corner.
Second, weapons that threaten 5 ft. around the character, also threaten squares that are diagonal in relation to the fighter, two squares diagonal from the fighter counts as 15 ft. of movement, so where does the reach fighter threaten diagonally if at all? One square away is 5 ft which is to close, and two squares in that direction is considered 15 ft. which is to far.
-check the FAQ. There is a special case when 10' reach threatens the 2nd diagonal.
Third, if I am fighting a large a large creature and I am standing adjacent to it with a reach weapon, if the square I threaten is one which he is occupying, since he takes up a 10 ft. square, but he is still adjacent to me can I attack him without moving?
-Yes. While you can't attack the enemy square that is adjacent to you you can attack on of the 'deeper' enemy squares as appropriate to your reach. Read up on the rules for reach and how cover is treated. Unlike ranged attacks there is no way to reduce the TH penalties (that I know of) for melee-reach-cover (such as having an ally between you and the target).
