Don't try to update the firmware from windows. It isn't the recommended method.
I'm not entirely sure what you mean by firmware or what you were doing. Do you mean, bios? Or were you simply trying to install drivers?
The preferred method to flash your bios: Your mobo should have a flashback port so you basically download the bios, put it on a fat32 formatted usb drive, rename the file to what the manual or website instructions tell you to, insert usb into flashback usb port and press the flashback button.
So basically what happened is you got windows to start and not all the new drivers for your rig are installed. Windows installs most of the system drivers automatically with plug and play (most of the time), and unloads the drivers from the old rig.
However I think first you should simply reset the cmos. Power off, and switch off the mains, clear the clear cmos jumper or remove the cr2032 coin battery for 30 seconds and put it back.
After that you should just be able to boot off your USB and run windows setup. Converting from mbr to gpt and then starting windows isn't the ideal way to install windows on the machine, for inexperienced users.
All the drivers from your old rig have to be unloaded from windows and the new ones installed. Windows doesn't automatically update the graphics drivers to the latest release only installs a generic vga driver and you get a low resolution.
If you can get windows setup to boot, run windows setup repair. That will sort out most of the driver situation then download your mobo and video card drivers latest version from the manufacturer's support website.