Hi,
Yes... that is what the tools in windows do... They give you a "Fresh" installation...
What I am suggesting is running your installation media from within Windows after the machine is running...
This works exactly like upgrading to a newer build and keeping everything... It is not exactly "Fresh" because it retains stuff..
You would want to run this either from the DVD, or with a Virtual Drive and using the ISO...
If you right click on the ISO you should see something about "Mount"...
If you don't, select "Open With" Windows Explorer... This will create a temporary Virtual Drive on your computer...
We need to get the flash drive out of the picture...
There is a chance that any type of repairs as we mentioned may not fix the boot files, but it should... It needs to restart for the upgrade several times and should create new boot files...
If you do this, unhook the HDD...