Have you checked task manager? If not, when things start to get slow quickly pull it up (ctrl+shift+esc) to see if any processes are using a lot of a particular resource.

If you want the drives to be useable, you’ll want to use a program that overwrites the data. This is important because when you “delete” a file you just remove a link to it but the actual data still exists and getting it back is trivial. Ideally the program will do a couple passes, overwriting the data with garbage.

There are tons of programs that will do this, which one you should use depends on your OS and whether the drive is an HDD or SSD.