I would suggest you do this:
Buy a couple of hard drives. On the first one, copy the "Music" folder in your main user or home folder and all it's contents to one of the new drives as a safety backup. Once done put it aside for now.
The main goal is to open each Logic Pro song, and do a save as, then resave to your additional new drive. When saving make sure you do a few things...
1) open your audio bin, and under the edit menu choose the "select unused" command, then press delete. This will remove any files you are no longer using in the song from your bin.
2) Select the "save a copy as" command, and make sure when you save that you select the 2 checkboxes: Include assets and copy external audio files to project folder. Then save to your new drive.
Once you have done this, you should have your new drive full of your songs, with only the files needed to play each song.
Once you have completed this stage and made sure each song will play back, you can go to the "Music" folder in your user or home folder, and throw out the originals to clear off space on your main drive.
You actually have backups now, a very good idea these days since Apple just had a recall on some of the drives that went out with iMacs... meaning any drive will die for sure. It's not a matter of "if" it's a matter of "when".
I'm not sure if that is what you meant about your song files and being disorganized, either way I hope this helps.