Problem With New Install

This is my setup. I have Windows 7 installed on a 128 SSD in a single partition: c:
I have an 1 TB HD, e: which is my data drive.
Using a registry tweak, I moved the "users" folder with all included sub-folders to the e: drive.
I installed Ubantu on a second 64 gig SSD.
I ran BCD up to the point after writing the new bootloader to windows.
I re-booted and the booloader came up in windows as it is supposed to.
However, when I picked is supposed to take me to a second did not.
Now, I cannot get inot Ubantu.
I don't know what I did wrong other than perhaps the fact that my setup is different in that it is not duel booted on a single drive.
I did not backup the bootloader.
How can I fix this?