It's kinda hard to make out the diagram... how about this?
As for arm pivots and turret pivots being in different locations, none of my turret's arms are centered.
Ok let me see if I got everything right... sounds like you did though
1. you placed the firepoints, firepoint and helper on the model.
2. aligned "helper" with the turret base's pivet point (in Max you can use Alt-A for quick align)
3. aligned "firepoints" to the turret's arm pivot point
4. placed the "firepoint"(s) to the turret barrel end(s)
5. linked everything correctly.
If the turret's firepoint(s) normal is pointing in the wrong direction, that's an easy fix.