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#11
You can leave windows firewall as it is.
Do not boot from the flash drive. Repair (upgrade) install can only done from within your existing windows.
Start into windows normally. Plug in the flash, then run setup from the root of the flash drive. It will say Setup is starting". When it asks , select "Upgrade installation."
It might take quite a while. It gathers your files and settings, moves your current installation into a folder called windows.old. It expands the files from install.wim onto your C partition, adds in the files and settings. It reboots a few times during all that.
If you have a lot of settings and programs installed it could take a couple of hours or more.
You will need to reactivate windows with a valid product key.