Download EasyBCD, and see if that will fix your problem.
It will let you place the boot files where you want and make virtually any changes to your boot system.
It's very easy to use.
I'd recommend that while you are doing this that you place Windows on its own partition. This will become drive C:\.
Once you are set up and running, make a system image of the drive.
Don't put your software or data on the same partition.
If you have any issues in the future, you can replace the whole drive including the boot sector in a matter of minutes and have your computer up and running again.
EasyBCD
The free version,
EasyBCD helps you take control of your boot loader. EasyBCD supercharges your Windows PC, allowing you to dual-boot to your heart's content.
www.majorgeeks.com
Backup software, EaseUs Todo...