Windows 10: windows booting on the wrong disk

So i have 2 SSDs, one i came with the PC and had windows on it, later i decided to upragade SSD and clone the original SSD to the new. After i had cloned the SSD, I decided to keep it in my PC and disable it through the device manager. Last night i was trying to solve some issues and accidentely turned on "use original boot configuration" on system configuration. After restarting the computer, it seemed that windows to separated into both disks as it shows on macrium reflect.I cant seem to fix this, i tried to do a scan and repair the OS with cmd, but it says theres nothing wrong with it. I

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Windows 7 booting off wrong drive?!?!?

Please move if this is in the wrong place.

I have two hard drives, a 1.5TB drive, and a 160GB drive. Windows is installed on the 1.5TB drive, as are all my files and programs. The 160GB drive has a bunch of old files, and apparently the bootmgr and boot folder. Nothing else is on the 160GB drive, other than media files etc.

If I remove the 160GB drive from the machine, windows refuses to boot, plug it back in, it works fine. The setup with two hard drives I have now is temporary, as the 160GB drive will go into another machine.

My question is, can someone give me a step by step on how to make windows force to boot off the 1.5TB drive, ignoring the 160GB drive in the boot process completely?
I don't know how to do this in Windows 7, on XP I would just run the /fixmbr command and its related ones.

Any help would be appreciated.

Note: I would really really rather not have to wipe and reinstall, I know it can be done without one as I've had this issue with XP before.

 

Can't safely remove external disk

In reference to the steps of your suggestions:

• The issue is specific to the particular disk and it started after I've used the disk to save the System image backup (created with the Control Panel > File History tool).
• I didn't disable any windows Service. I'm just wondering if there is any to disable.
• Safe boot with networking, or clean boot doesn't resolve the issue.

Thank you.

 

Installing windows off of a USB stick

Step By Step from vista:
From admin cmd prompt

1. diskpart
1a. list disk
2. select disk 1 (replace 1 with your usb drive)
3. clean
4. create partition primary
5. select partition 1 (replace 1 with your usb drive)
6. active
7. format fs=fat32
8. assign
9. exit

Copy Windows Vista's DVD ROM content to the Flash Drive

xcopy d:\*.* /s/e/f e:\ (d being your vista cd and e being your usb stick)

And that's it, boot off your usb disk