Well, first and foremost: Get yourself an external USB backup drive!!
They are so cheap these days and not having a backup is playing with fire. If you value your data you must have at least one backup, ideally you'd have two, with one either in the cloud or on a drive that you store in a location other than where the first copy of the data is. I realize that most folks (including me) don't do that, but I do keep two copies on two separate backup drives that I alternate each month and keep in a fireproof box.
None of your user data should be under any of the Windows folders anyway. User data is typically under C:\Users (which will have a drive letter other than C: once your old drive is transplanted). If you don't need the space then don't delete the Windows folders, but if you need the space I wouldn't hesitate to nuke it on the old drive that's going to be your data drive.
Remember if you are taking backups, and they're full system image backups, and you're storing the primary copy of any data on that transplanted drive, you need to include that transplanted drive as part of the system image.
I would also suggest using the excellent File History feature built in to Windows 10 to take user data backups from the folders where you store things.
You have got to get a backup drive and start a cyclic backup protocol, and then follow it.