Hi cbrillow, first of all, since you have done a reinstallation, please make sure you have installed the latest patch 1.11.7.21 which you can find here http://www.aerofly.com/downloads.html

When you go to "controls", in the "aircraft control settings" page, make sure that the dot for the new usb interface/GC corresponds to "aircraft 1"

Then go to "properties". You should be in the basic channel asignment page (If you are new to AFPD I would suggest that you use the basic channel assignment. When you are more experienced, you could use the advanced chanel assigment). Move your controller sticks and you should see the bars at the bottom moving. Assign one channel at a time e.g. start with your elevator stick, move it and see which bar moves. Then place the dot at the position corresponding to elevator function. Do the same thing for rudder, aileron, throttle, etc. Then do a calibration (place all channel trims to the center). Then fly your model. If you find that there are any function that are reversed, then go back to the controls page and tick the reverse box. You must do a calibration again.