Windows 10: Windows 10 not booting on drive it is installed within + more

As said in the title, my Windows no longer boots off the SSD it is installed in C: Drive. When I restart my computer, it says that Windows 10 is not found within the SSD. Interestingly, if I manually boot off my HDD D:, the system boots fine, Windows is fully operational and all my files and data are present. This has only happened after I made my C: drive my Active drive in Disk Management. I did this because I thought it was what I was supposed to do, as I researched what it meant and thought it applied to the drive my Windows boots off of. To add more information, neither drive in Dis

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Is it time for Windows 10 already?

Here's a good step by step guide on doing a fresh install.

How to clean install Windows 10 from a USB drive - Software - Feature - HEXUS.net

 

Windows 10 boot drive

Is Windows 10 also limited to a max of 3Tb for a boot drive?

 

Windows 10 USB boot

Hi there, am not a windows 10 expert. I have a pc in the bedroom on windows 10, I messed up the bootloader trying to fix the xp on that system.

System wont boot, trying to repair via win 10 usb installer.

Downloaded the media creation tool to install windows 10 installer on usb stick. Not compatible with a host of usb sticks I have. Tried the usb sticks that others use, but I think they use rufus; as the media creation tool by win 10 does not detect the usb stick.

So quick question, the win10 machine i am trying to repair the bootloader is a win7 upgraded to win10.
If i were to use the usb win10 installer to "repair installation" does the version of the iso downloaded via the media creation tool matter?

There is three options:
Windows 10
Windows 10 Home
Windows 10 N

Also is there a step by step instead of using rufus as I want to try an alternative method of creating a usb win 10 installer. Preferably with more compatibility.

System is a asus sabertooth 990 (r2?) with AMD phenom X 6.

Also is there any other software I can load onto the usb that can repair the bootloader easily?
That would be the ideal alternative. Thanks