If you have toe brakes working, I assume you have USB pedals.
Just to make sure, have you looked in the AH mapping interface for your pedals? They will be a separate device if you arent using the Control Manager software. Find the drop down list that says ........... whatever it is now, something like "Controller" or "Device". Your joystick should be there in that list, along with the axes to be set and what they are mapped to (ie "Y Axis and X Axis to Pitch and Roll, etc). Z axis in THAT list is your throttle on the stick. Ignore that and set it to nothing if you have a HOTAS. It's meant for a "up/down" slider, not a 3 position sliding setup like a rudder. In the drop down menu you will either have the rudder pedals listed, or a ? for an unknown device. Select it and set your Z axis on that controller, and try again.
You can alternately use the Control Manager software to combine all your devices into one device for Windows. Then you'll see two "Z axis" settings on your stick in Aces High. One will say "Z axis" and one says "Z rotation axis". One is your stick throttle, one is the rudder pedals.