reply to Mina
Re: question about malicious software Install malicious software first; yes when setting up the boot partition with tools.
However for your question....I think you may have a little info missing or didn't understand what he did.
1. A new clean HDD doesn't have the O/S on, so where did the installer come from?
2. He may have tried to boot straight off the USB stick to install, then found it wasn't detecting the system (USB) correctly, booted into the bios/diagnostics, changed the boot order then went about booting and installing everything in the correct order. That is very normal practice.
Nothing unusual, but with out the specifics of the process and the bits you are missing, then we can't really help say yes or no.
I can offer tools to scan etc, but really to see what happened someone would need the computer, as a specific tool or script loaded may fall outside of the detected malware out there and a specialized look a the computer would be required.
If you want to install everything your self, request this moved to the Microsoft forum and install the O/S yourself. If there is no warranty concerns and you do not need or require warranty for the next time it breaks, someone can help there guide you through installing the O/S on a new HDD for you. As long as you have 2 computers, 1 to talk with the forum and the computer in question.
The only thing necessary for the triumph of evil is for good men to do nothing - Edmund Burke