Michael Sayre
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No, Flurry allows you to act as though you already had TWF, so they do not stack.
"Flurry of Blows (Ex): Starting at 1st level, a monk can make a flurry of blows as a full-attack action. When doing so he may make one additional attack using any combination of unarmed strikes or attacks with a special monk weapon (kama, nunchaku, quarterstaff, sai, shuriken, and siangham) as if using the Two-Weapon Fighting feat..."