My fs9.cfg is here.. C:\Users\Robin\AppData\Roaming\Microsoft\FS9
The other new cfgs will be in that folder as well.
So, if you have a second or third FS2004 install, each install must have it's folder, so you will have FS2004, Golden Wings & Silver Wings, as examples. I have 5 different FS2004 installs.
Please install or copy & paste the sims into C:\ & NOT in C:\Program Files.
The FS9.exe MUST be uniquely named as well, so, in each additional sim folder you must rename the fs9.exe, so you will end up with an FS9.exe, a GW.exe & a SW.exe
You will therefore have separate cfg's, such as fs9.cfg, gw.cfg & sw.exe one the sims are run.
To find them might be a bit difficult. Download a little program called Everything from http://www.voidtools.com
This is, in my opinion, the fastest desktop search engine out there, & after running it, when you start typing, it will display the search results immediately.