By "indesign 2", do you mean CS2, or literally version 2. I'm assuming CS2 since I know v.2 won't even run in Snow Leopard.
If you pared the fonts down according to my article, then that means you manually moved or deleted fonts from the hard drive. Font Book is a very unhappy camper when you do that. It seems to be unable to correct its database when fonts are moved around by the user.
Restart your Mac and immediately hold down the Shift key when you hear the startup chime to boot into Safe Mode. Keep holding the Shift key until OS X asks you to log in (you will get this screen on a Safe Mode boot even if your Mac is set to automatically log in). Let the Mac finish booting to the desktop and then restart normally. This will clear Font Book's database and the cache files of the user account you logged into in Safe Mode.
Next, close all running applications. From an administrator account, open the Terminal app and enter the following command. You can also copy/paste it from here into the Terminal window:
sudo atsutil databases -remove
Terminal will then ask for you to enter your admin password. As you type, it will not show anything, so be sure to enter it correctly.
This removes all font cache files. Both for the system and all user font cache files. After running the command, close Terminal and immediately restart your Mac.
Things should be working correctly at this point.