Blinking Cursor with Windows 7 bootloader

So I got myself into a bit of trouble with the Windows 7 bootloader.

I have a dual boot system with Gentoo Linux as the other operating system. I have Linux installed on partition 1, swap on partition 2, Windows on partition 3, and a storage drive as partition 4. Partition 4 was NTFS format, but I formatted and encrypted it.

Turns out unbeknownst to me that the Windows 7 bootloader was installed on partition 4 and now I cannot boot windows. Windows was apparently installed on a logical extended partition for some reason, thus it had to use a different drive to install the bootloader on.

I tried using my Windows 7 recovery disk and the automated startup repair didn't even detect the Windows partition at first, but running bootrec /scanos from command line did detect it.

I used Partition Wizard to convert the Windows partition to a primary partition and marked it as the only bootable partition in the whole system. After doing that the windows installation was detected by the automated repair wizard, but it is no longer detected by bootrec /scanos.

I have done everything from this guide: Recovering the Vista Bootloader from the DVD - NeoSmart Technologies Wiki

All I get when I try to boot windows is a blinking cursor. I'm at a complete loss for what to do, but I figured that this would be the best place to look for help.