Make programs work again
Uhhuh. I don't see how you could achieve all this post-humorously. Regardless of where the files for the installed program are located, a portion of it will always reside on the same partition as the operating system. Most common locations are %appdata% C:\Program Files\ C:\ProgramData\ and the Windows registry in addition to the obvious Program Files and Program Files (x86) -folders. Souds to me, you've now lost all or parts of the date you had in there. Hence Windows doesn't know what you preferred programs were, what programs had access to the right-click menus and so on. Heck, as it stands, Windows doesn't even know you have VLC or WinRAR in there. Some of your programs might not even work anymore (possibly blurting errors like can't find .DLL this and .XML that and so on) and some may only lost variables like save states and user preferences.
To counter the effects of this mismatch, you should have migrated the programs. The process involves preparing the programs before the re-install. You now, getting all the relevant data from all over the place into one compressed file and then after reinstalling, un-compressing it all to where it belongs. But by the sound of it, it's too late to migrate. You'd require access to the old OS.
None of this isn't to say that you can't get your settings back via manual registry edits, getting the matching files from the developers or us even and so on. All manually one by one.
Tl;Dr: If I were you, I'd get my re-installing pants on rather now than after hours/days of hunting after fixes to each individual issue.

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