"joystick does not get the thing moving and I can't fire or move guns"
In controller mapper if you have "auto select mode at start of flight" checked, but do not have anything mapped for mode 2 (vehicles), you'll have that problem. Copy mode 1 (there's a button for it) over to mode 2 and problem should be fixed.
"I'm having problems getting some of the key commands to work when in flight (bombsight calibration, external views, parachute, etc.)"
External views for fighers are disabled in the main arenas. For chute, your joystick should work for turning, but I believe you have to map something to make you move forward and back. Not all "bombers" have a bombsite position, some are purely designed for divebombing.