HELP, Computer issue

I posted a previous entry in a forum about my EDGE SSD not showing up in the BIOS,
well turns out the SSD was shot, so I replaced it and got a new Windows 8.1 operating system.
The new SSD is a ADATA XPG SX900 128GB SSD.

Now here is the new issue that has appeared:
All my files on the old hard drive are there, however, there are a lot of weird things showing up.

Example: All my Witcher 3 saves are gone, and when I reinstalled it for a new playthrough, it said I have absolutely no Witcher 2 saves to use for a new game. (Saves are showing up in the hard drive)

Example 2: Elder Scrolls Online is not working properly and won't open.

Example 3: Error codes are shown to me when I try making a desktop shortcut.

Yada yada yada you see where I am going.

Either way, I would like to know if there is a possible fix for any inconsistencies with the new SSD and my old Hard Drive, or if the old Hard Drive just needs to be wiped and start anew.

Let me know if you guys need me to be specific on anything, all advice appreciated.

@yetisnacher I suggest you run a virus scan first ( highly unlikely of a virus activity). Also, try booting your system without the old drive and try placing a shortcut on the desktop.

Did you do a direct clone or a reinstall and then copy over your data from the old drive?

This seems like a folder permissions issue; what error code/message are you getting when you try to make a folder on the desktop?