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I have a drive with a windows 8.1 install that got pretty mangled after I accidentally installed linux mint to the whole drive instead of a partition for dual boot. I canceled after a split second, but the damage was done. No files or OS installs were available at all. The main concern is to get back the files that are not backed up.

I used Testdisk and the deeper search, which allowed me to see the file structure that revealed most of my data. I was able to undelete this and can easily copy it. However, I'm still missing a few key folders with a large amount of data (definitely not overwritten). The drive size shows as about 550 GB, but in the folders there is only 330 GB of data - some folders are empty.

How can I see and copy this last data that seems to be hidden? Any help here would be greatly appreciated!

You can run "cmd" (right click run as administrator) and "chkdsk /f d:" (replace d: by the correct drive letter). It should move your lost directory in a found.001 directory. As it's a gamble, you may prefer to try other data recovery utilities first.
In the worst case, chkdsk will delete all the lost files and you will be able to use PhotoRec to recover files from the free space but filenames won't be found.

Well it looks like I've got another wrinkle. I thought I could copy the files, but many of them have input/output errors when trying. So while I can view those easily in linux, I don't know if I can get them off! So it looks like it may be a bit more than a lost directory.

I am currently working on backing up the image so I can run it through some other programs on a windows machine (can't get a live boot of windows working here). Having the problem of MBR/GPT mismatch on clonezilla, so looking for another way to copy and not just take the artificial partitions other programs will send me out with.

Any thought of whether that would work? Going to run it through GetDataBack. Hopefully that can restore some of the file structure and at least allow me to pull my data out.