Just remember that when you run Link Removed, all the non-Win 8 Style apps will be uninstalled as a part of the Refresh. A list of uninstalled apps will be created on your desktop. I believe all customizations and user settings and data are preserved.
Just make sure you have all your installation files and keys available before doing the Refresh.
It definitely sounds as though something is wrong with the basic Win 8 system that is preventing the Win firewall from starting. See if it starts after the Refresh, before installing any of your apps. If so, check after each app is installed to ensure it is still working.
If the firewall does not start after the Refresh, I would suspect your ISO file download may have somehow become...