Focused Specialist is a wizard base class alternate class feature, and hence should only apply to that IMO.
Even the conversations I found only gave you the extra slots once (but as a Dual Specialist, you got to pick which school to put in any given bonus slot). I agree, you should only get the bonus slots once, and given the way 3.0 Incanatrix picks up the extra school specialization, the focused slots should only apply to your original school. (As per clarification from the writer, Sean K. Reynolds, you don't have to pick abjuration spells with your two free spells per level, but do get the bonus spell slot per day).
So, if a normal wizard got 4 spell slots of a given level, a specialist would get 4+1, a Focused Specialist would get 3+3, and a Focused Specialist/3.0 Incantatrix would get 3+3+1 (but have four prohibited schools).
Sounds good and reasonable to me. Just wanted to make sure.