The setup.exe should have opened a window which asked how you wanted to install. If you run the setup from the Windows desktop, you picked the correct one, it should have finished. I just did the procedure a couple of weeks ago on one of my systems. If you want to look the procedure up to confirm, maybe look for in-place upgrade or repair install.
All I can suggest now is your install is corrupt enough it is having serious problems and a clean install may be your only option. Maybe you could get a new drive and install to that to see what happens. At least you would still have the current install if you wanted to go back