Hello dhasdell,
You are going to have to set most of the controls yourself. I am just going through this myself. It can be a bit clunky but it can be done!
Navigate through Options/Controls/PlaneControls. Here you see all the things you can set yourself.
Find the "Engines control: throttles" option .
Look at the 3 boxes to the right of the "Engines control: throttles".
One of the boxes should show "minus/equals" that is the keyboard commands for throttle up and down, leave that one alone.
If one of the other boxes show a joystick assigned you need to re-assign it because it is not working with your joystick, or if they are both blank you need to assign one to your joystick.
Left click where you are making your throttle assignment.
(clicking in a box with an assignment will re-assign it, clicking in a blank box creates a new assignment)
A dialoge bow will open;
------------------------------------------------------------
Push device button or move axis to assign
Engines control: throttle
mouse_axis_Y <------watch for this guy (may be slightly different for you)
APPLY RETRY CANCEL
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The difficulty here is that it almost always detects a mouse movement at this point and offers to assign whatever option you are trying to adjust to the mouse.
So click on RETRY, then imediatly after move your joystick throttle forward.
Hopefully the game detected this and the line that said "mouse_axis_Y" should now read something like "joystick1_axis_2". If so, hit apply. It may still offer the mouse just keep hitting RETRY and doing it over until it works. (Hold the mouse real still when clicking RETRY)
Repeat this procedure for any other assignments you wish to make.
I hope this helps,
Rob