In many years looking how to speed up Windows systems, I came to this conclusion draw from experience: if I run a utility to "wipe" or to "compact" the MFT, the system will run snappiest than ever. That should be done along with the rest of the other steps. Windows do spend a lot of time going through that MFT for its file accesses. If you have many many files, lets say from having temporarily backuped user files or that kind of thigns, your MFT is bloated and a treatment to it will do wonders. Alas there are very few utilities to do that. I have found R-Wipe&Clean and a product from Paragon.
Best regards,
Roberto