What to do if after your MacBook Crashed & iTunes over writes your media folder

So my MacBook Pro hard drive was starting to fail, and before it died I copied my music through itunes over to an external drive. I reformatted the drive, updated to Mountain Lion & have started to get back to "life as normal" after having to reinstall all my programs and what not. I didn't have enough room to back-up my entire to the external, so I trashed my music & I ran time-machine to back-up the rest if my drive. 
I started up itunes holding down the option key & directed it to my external & was stoked that everything was still there. Included all my playlist. Life seemed good. Enter sad Thursday....
For some reason my MBP crashed & I had to reboot. Upon restarting all the windows and apps opened up to what was either open on visiable before the crash. I noticed the itunes jumping in the dock, so I went to check on that. I redirected back to the folder on my external that had my music & thought all was good. Now there is no music in the media folder. I think I've lost all my music. I run Disk Drill and was able to find some of the files, about 50% of my music. I'm left still looking & trying another data recovery app to see if I can put it all back.
Has anyone have this happened? Is there a fix?

Ipod does not appear in iTunes may also offer helpful suggestions.
Usually, I just recommend a reset while the iPod's attached to the computer. Easier, no?

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