Hm, do you remember what file you downloaded? IIRC there was a problem with using FDE's (the aircraft.cfg and .air files) for FS2002 with FS9, which was fixed when AIA released an update.
An alternative idea would be to download the unofficial FDE update from Jan Martin and using that. Go to http://janswebsites.110mb.com/flightsim/index.html
and scroll down to the 'Jan's FDE's' section and download the file called FDE's For AI
Unzip the file to a temporary folder, open that and find the AIA B732 folder inside
Copy the aia732v5acofadv.air file to the AI
Aardvark 737-200 folder inside your Aircraft folder.
Rename the aircraft.cfg in the AI
Aardvark 737-200 folder to something like aircraft.cfg.bak or aircraft-ORG
Copy the updated aircraft.cfg file from the AIA B732 folder to the AI
Aardvark 737-200 folder.
Open up the back-up aircraft.cfg file and copy the entire fltsim.x sections to the new aircraft.cfg and then save (make sure it doesn't become aircraft.cfg.txt