Restoring programs/registry etc without full image, only files?

I am about to do a factory reset and reinstall of windows since I could not get the previous installation to boot due to a failing hdd. I could not make a clone or image because if macrium/acronis or any imaging software encountered a bad sector it would quit immediately. Instead I have a copy/paste of the all program files, system32, user data etc on an external hdd. Most of the data is readable and I suspect I couldn't get the previous installation to boot because of corrupt system32 files that SFC couldn't fix.

I am doing a factory reinstall but what is the best way to restore all of the data? I couldn't boot into windows to make a .reg backup, so I don't have one. Is there a way to make a registry backup if you can't boot? I still have the system32/config folder and everything, and I want to at least get back some product keys from the registry using Magical Jellybean program.

Since I'm reinstalling everything, I'm assuming I can't just copy and paste the program files or appdata folders back? If I could manage to restore some of the settings it would be a lot easier.
I only know for some programs, like Steam and Firefox, I can copy and paste back my userdata folders and restore settings like shortcuts, bookmarks, addons etc.

Also, I saw that Ccleaner has a useful tool to create a list of programs installed and export it. I tried running Ccleaner from a usb bootable environment but of course it only works if its installed on the system. Anything similar that could scan for installed programs if I can't boot?

To reiterate, I don't have a clone or image, but I do have a straight up copy&paste backup of everything on my windows 7 partition and almost all of the data is readable.