Using MozBackup you will be OK it will put Firefox back to the way you had it.
For your themes follow this tutorial Theme Pack - Create, Save, Install, and Delete
if you have some custom themes you will need to go to C/Windows/Resources/Themes and copy them from their. If you need more help with either of these just ask I have done both many times.
You can copy your drive sector by sector and you should have everything there.