I think I have found the easiest way yet to have and access multiple FS2004 installations on your system.
I was looking for a way to have two installations of FS2004 on my system and be able to select one or the other by clicking an icon on the desktop. I found a pretty easy way using a DOS batch file.
1. Copy all the files in the Flight Simulator 9 folder to a new folder called FS9a or something like that...your choice.
2. Opened Notepad.
Type the following:
"c:\program files\microsoft games\flight simulator 9\fs9.exe"
3. Save the file as FS1.bat into your Documents and Settings\(your name)\Application Data\Microsoft\FS9 folder.
4. Copy FS1.bat and paste it to your desktop as a shortcut. Name it FS1 or whatever you like.
5. Open Notepad again.
6. Type the following:
"c:\program files\microsoft games\(whatever you named the new folder)\fs9.exe"
7. Save the file as FS2.bat into your Documents and Settings\(your name)\Application Data\Microsoft\FS9 folder.
8. Copy FS2.bat and paste it to your desktop as a shortcut. Name it whatever you like.
Now, you just have to click on the appropriate icon for whichever installation of FS2004 you want to run.
The DOS window will appear momentarily on your screen when you start the sim and then the version of the sim you chose to run will startup.