I'm not entirely sure, but I'd say that you cannot combine TWF and Flurry of Blows in any case. If you want to weild 2 non-monk weapons effectively, you will need to take TWF, since you can't flurry with non-monk weapons.
I believe the idea behind the flurry is to allow monks to attack with both hands and/or feet/knees/elbows, like they had the TWF feat, tho it only applies to the select weapons they train with.
My question has always been: can you flurry with all your attacks with a single monk weapon. I'm 12th level, and get 4 attacks at +9/+9/+9/+4. Can I attack all four times with my +2 Keen Kama, or do I have to use both hands?
The Dread Pollock