0xc00000e9 error, Unable to boot to windows, help?

I suspect you will end up replacing the hard drive, but let's not go there now. Boot from the USB drive and on the third screen, in the bottom left you will see 'repair my computer'. First try running startup repair. You may need to run it 3 times with attempted reboots into windows between each time. It will try to re write/restore/repair any missing boot files. If you are using the installation USB this is step by step instructions System Recovery Options
If you are using the repair CD this will tell you how, it is really the same Startup Repair.

You cannot install Windows from a recovery CD, but you can try to repair your computer. With an Installation DVD you can repair your computer the same as a recovery cd will, but you can also install windows with it.

What are you trying to run? Seatools, Repair disk, installation disk? Are you doing it from an ISO or from a disk?

Here is the easiest way I know of. If you don't have it, download 7 Zip (free) 7-Zip. Watch out for any add ons they throw in with it. in Computer highlight your USB flash drive and select Format, take the quick format and click restore device defaults. Highlight the ISO file, right click it, and put your cursor on 7zip, you will get an expanded menu from there, select extract files, in the search box go to your USB drive and select it and press OK, it will start extracting the ISO files to the USB drive. It will take maybe 1-2 minutes. When it finishes, it will be bootable. I just tried it and it works just fine.

Wish I could.