Messed up boot up harddisk. Need help to repair.

Hi JoshuaAvalon, welcome to the Forum.

If you disconnect SSD B, will the computer boot up?. If it does can you make a screen shot of your SSD A. To that follow this tutorials on supplying a screen shot.

Disk Management - Post a Screen Capture Image

Screenshots and Files - Upload and Post in Seven Forums

Also what size are both of the SSDs?.

What program did you use for the clone?.

Your problem is that the System Reserved should be on the Disk that has C: with your Active. If you make that change you should be OK. Do you have a Win 7 Disk? If so then follow the Tutorial Startup Repair == Before you do that, there is one important thing that must be done. The reason your PC is messed up is because you had more than one Disk plugged in when installing Windows. After you boot your PC and before you begin Startup Repair, open your PC and unplug all Disks except for the one with C:. Run the Startup Repair, boot your PC with only C: plugged in and let us know if it booted. == Just as info, doing an Image is more reliable than a Clone. Macrium Reflect is the best software and it is free. Macrium Reflect Free

JoshuaAvalon said:

No, it does not work.

For further investigation, I try to boot up from C:. I found that it is fine.
I assume that is because Window ( F: ) thinks it is boot up from C: (which is not)

What does not work, booting? Then you say that C: is fine. You have me confused. == If System Reserved is not on the Disk with C:, it is NOT FINE. == Did you run Startup Repair?

JoshuaAvalon said:

No, from my msconfig, it said current OS is from F:\Windows. Also, if I try to boot from C:\, it has a text on the bottom right saying my window is not valid. Therefore, I want to fix the F:\Windows

I have asked different questions. You have not answered them. You only tell me stuff you have done. I can't help. You want to make Windows boot from F:. Can't do it. If you want help, you need to follow us and answer our questions.