Windows 8 - All of my permissions are broken

Question

Windows 8 user here, and when I first started up my new computer, I discovered that almost all the permissions were broken. I did not have write access to several key areas, such as the root directory of my C drive and the startmenu folder (which is required by 70% of installers)

I used a batch script to Take Ownership of all the files on the hard disk, which has made the computer more than useable for the last 4 months, but there are still a lot of issues. The main one is that most of my Services will not start correctly.

I have fixed a couple of these broken services manually (such as Base Filtering Engine, which is a dependency of Windows Firewall) by navigating RegEdit to HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\[something] and giving NT Service/[somethingelse] Full Access. Note that [something] is sometimes related to the process name, and other times just SharedAccess. Also, [somethingelse] has so far always been strongly related to the process name.

What I'm wondering is:

• What do I need to give permission to in order for Windows Installer to work properly?
• Is there something I can do to fix all the permissions?
• Failing that, is there a way to find out what specific permissions are causing a specific error? (Error 5: Access Denied)