To backup your license, simply log in with winbox and export it to a file. Later when reinstalling any version of RouterOS (compatible with your hardware!!!) The unique SoftwareID should be the same. You should be able to then import back your license. Furthermore, it should be kept in your mikrotik.com account, so even if you don't have the "file" - you should be able to retrieve it anytime from your mikrotik.com account.
Consider upgrading to ver. 3.17, as our dear friends at MikroTik may have fixed a lot of problems in this new release. I hope
To backup your router configuration, log in with WinBox, open a new terminal, enter the command "export" then right click, "Copy all" and paste the contents to a text file. A little edits to the textfile, and it will be ready to be pasted back in your router, in case configuration is lost. Paste back little by little, so that you would be able to see if there's an error and correct it.
After upgrading to v3.17 if you still have a problem - look at the forums for solutions at the same time contact MikroTik support at their e-mail, providing a supout.rif for them.
P.s. I myself reinstalled the latest 2.9 release on two of my routers recently, in my case they ran faster than v3.15 & 3.16 - but my hardware is old x86. What's your hardware?