I've only administered the FP extensions on the NT side but I suspect there are some similarities. On the NT side, FP uses certain executables to do a lot of the work. You have to set permissions on the directories that contain these executables so the web server can read and execute the files. Most of these are in the /_vti/bin/ directory I believe.
If this was working until you re-installed them, I would suspect that the problem is not with the Apache config since the install would only affect the FP files and their directories. Do the install directions give you any reference to what the file and directory permissions should be? If you're new to linux/unix, you'll be looking for something like "chmod 777", "chmod 650", etc.. As a test, you could do a "chmod +rx FPDirectory" where FPDirectory is the install location for the FP files. If this works, then it's just a matter of finding out what permissions the directories should have. Be very careful with this as a lot of security holes revolve around executables and directories have more permissions than they should.
GJ