To the original poster:
Here is the procedure I think you could try. Use PTR2Cache GUI (
http://farc.3synergy.net/misc/p2cgui.zip) to create custom cache files (I like to use the cache.m, but back up your original first!) so that you can extract files using the toolkit, that normally aren't savable. The files will appear in the Missions menu in the Toolkit. I haven't tried it yet but PTR2Cache should work with the ATF Gold TK.
OF COURSE THE MOST IMPORTANT STEP OF ALL TIME IS TO FIRST, BEFORE DOING ANYTHING, VIEW THE MISSIONS LIST IN THE TOOLKIT TO GENERATE THE CACHE.M FILE IN THE FIRST PLACE!!!!!
The files I think you should focus on are the .XMI files. They will have names such as AIR014.XMI. Use PTR2Cache to first select LIBPTR.XMI, and then select CACHE.M. It will make the XFI files appear in the M file type cache file, accessible in the TK. Double click to try saving them in an ATF Gold Toolkit project, and then copy the files from the project folder (TOOLKIT\PROJECT\PROJECT NAME) to a FA toolkit project folder. Copy the lines in the ATF Gold Project's ITEM.DAT (also in the project folder) to the FA Project's ITEM.DAT (paste at the beginning of the text in the file to avoid crashes in the Toolkit).
There are also .MUS files, which if I had to guess they are music control files. The library Cold War Fighters had custom .MUS files and custom .11K files with titles such as XFI105B.11k, which appear to be the custom music files, maybe the are only for menus???
When I have more time I will try to follow the procedure above, in the mean time please post any questions or problems you encounter.
Zephyr