I know this is a massive thread mine, but I think it is important that I post the solution I found to this problem.
I had exactly the same issue - I moved my iTunes music folder and music library file to a custom location on another hard drive.
PS3 Media Server was no longer able to find the file, and therefore I couldn't access my iTunes library on my PS3.
So what I did is this:
I created a symbolic link from the old (default) location to the new (custom) location of the iTunes media library.
I did this in Windows 7. I understand this is the Mac support forum, but I believe it should still work in Mac.
You'd have to Google the procedure to create the link, sorry.
Once you have created the link, restart your PS3 Media Server.
(I believe this is also possible in Linux.)