I feel like I should clarify some of the things here to give you some peace of mind.
Any idea why when I booted my PC, I ended up in the Gigabyte title menu, and my keyboard was not working at all. I changed the USB port and after some time it worked. Then when I go to the Windows longon screen, neither my keyboard nor my mouse worked, I waited maybe 3 or 4 mins and then both worked without me doing anything.
This happened the first time I booted this new PC yesterday.
Also; any recommendation for a really quiet fan? I used one of my old ones and it turns out it's very loud.
Most likely, those USB slots were not initialized yet. Most motherboards come with just a couple of "internal" (for lack of better word) USB connections and extra chips to enable the other 4-6 USB slots that need to be activated or initialized before use.
Second part about mouse/keyboard not working: It's because you just installed a new motherboard. Windows probably didn't recognize any of the USB ports (after searching for the old ones) and had to install the correct/generic drivers before it could detect your device.
Yesterday it showed me the bios screen and asked to choose the hard drive,
today I got a black screen with a blinking white bar in the top left corner of the secondary monitor (the main had no signal) and it just stayed there endlessly.
Sounds like one of the hard drives wasn't connected. Just in case, I recommend unplugging and replugging the wires for the hard drives again from both ends.
The endless blinking is probably the computer trying to read/boot the hard drives but were unsuccessful.
...Either that or your hard drive is dying.
I rebooted, and then nothing came up at all, no signal for both monitors.
Once again, could be your hard drive is not connected or dying.
I shut it down and inspected, found no loose wires or anything, booted again and now windows booted, showed up on the secondary monitor, then no signal to both, and then the login screen appeared on the main monitor.
Any idea? I didn't reinstall windows after cganging motherboard/cpu/gpu, but I did install the drivers. Windows also asked me yesterday to do an online validation of my windows license and it said it succeeded.
Don't know what is happening:/
Sounds normal. If you have a SSD, sometimes Windows will boot faster than your monitor as it tries to auto-rotate between connections and detect a signal. Most of them try DVI first, then HDMI, then VGA/Displayport (not necessarily in that order).
On a normal boot-up, the loading screen is usually displayed on all monitors connected.
Also, BIOS (for any device) are not automatically installed or updated by Windows. You will need to visit the manufacturer's website to download and install it through a specific method as outlined by your manufacturer's manual or instructions.
(It doesn't matter how "new" you think your motherboard is, the BIOS is probably a few revisions behind after a couple of months of being produced.)