It might be possible to re-set all perms to allow from command line but that really depends if Windows wasn't too messed up to still be able to. Something like this from Windows recovery command line maybe: https://stackoverflow.com/questions/2928738/how-to-grant-permission-to-users-for-a-directory-using-command-line-in-windows However, mind you, if you mess up doing that or even trying it could potentially make things worse or not any better. Its not good to mess with perms unless you know exactly what can be done as even minor changes sometimes can result in total failures.
In this case and what I would do with perm catastrophe, you can get your files either way by using a non-Windows OS, copy them off to an external USB drive, then clean install Windows. I'm only telling you what you can do. I'm not walking you through any of that as its far too much and too varied and I don't really walk people through things anyway 99% of the time.
Someone else might try to walk you through something or suggest something a bit different perhaps should things still be somewhat working. If for instance you did something else that I'm not thinking about or understanding from your wall of text.
Hope the best :)