The following quote from the flurry of blows class ability prevents the use of additional natural weapon attacks along with the use of a natural weapon (using FCT) while using flurry of blows:
A monk with natural weapons cannot use such weapons as part of a flurry of blows, nor can he make natural attacks in addition to his flurry of blows attacks.
Feral Combat Training only modifies the first half of that sentence, it does not modify the second half -- that restriction still applies.
So, what basically happens is that if you pick Bite as your FCT choice, you get iterative attacks using the FOB progression applying the modifiers you have that occur with your bite attack (to each of your FOB iterative attacks), you then cannot use your bite attack as a natural weapon -- nor can you use claws, or tentacles or hooves, or any other natural weapon.
If you want iteratives and natural attacks, you get those without having to take feats or anything else. However, all natural attacks become secondary (-5 to attack and 1/2 STR damage bonus). And a monk uses is regular BAB on the iterative attacks, not the FOB progression and cannot use his natural weapons in the iterative attacks...those are unarmed strikes.
This isn't complicated.