How can I restore files stored in folders outside of a home directory

I recently replaced the hard drive on my MacBook Pro running OS X 10.9.3.  After I had re-installed the OS and created a dummy account, I used my time machine backups to restore all profiles on the machine.  This brought most but not all data I had on the machine.  While this is not something that will occur often I would like to avoid this problem in the future.  I had installed Mysql and I had one instance with data stored within.  After I had restored all of my profiles, I could not start the database instance.  I was forced to re-install the application, recreate the database instance, and re-insert the data.
I had made sure that I had backed up my data a couple of days before I replaced the drive so I thought I was save to proceed.  I have looked at the time machine preferences and there is no place for me to specify what directories to include in the backups only what to exclude.  This leads me to believe that the data in question was backedup.  I just was unable to restore it.  After I had it all working again, I was able to figure out that the data was located at "/usr/local/mysql/data/instace_name".
As I said before, this problem was generated when I replaced the hard drive.  I replaced it with an SSD.  For that reason, I know that I will go through this problem at a later date.  I just want to be proactive and plan for the failure of the SSD.
Thank you
Javier Salazar

I don't see why transferring the user account using Transfer Assistant at the time of the installation, would not have brought the information across.  It could be that making a "dummy account" has led to having a different user account number from the original account, with consequential access problems.  It is a problem met when using Migration Assistant after the initial install.
Pondini was the expert on all things to do with Time Machine.  Here is an article from his guide on transferring data.
http://pondini.org/OSX/Transfer.html

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