MBR fix for Windows 7 thinkpads?

I really need to resolve this issue. My MBR is "broken" (restored to a non-lenovo stock Windows 7 MBR) and now all my lenovo software and a lot of my hardware's software won't work. e.g. Intel graphics control panel, lenovo system update, lenovo power manager, etc... While loading any of these, I get "<application name> has stopped working....".
Background:
I previously removed a dual boot of Fedora I installed. However, the grub boot loader remained and I wanted to get rid of it. Normally Lenovo's Rescue and Recovery can be used to restore the boot loader (and remove grub), but I couldn't load R&R nor install a newer version. From what I could understand from reading online, R&R required the lenovo boot loader installed to work properly so I couldn't use it to restore my boot loader - a classic Catch 22.
I decided to borrow a windows 7 CD to use the repair feature. It worked by restoring windows 7's boot loader. However, ever since I did this, a lot of the preinstalled applications I listed above do not work anymore. None of the lenovo software work for sure. I have tried to reinstall some with no luck.
My best guess is that I can't use Window's MBR, but instead need to restore Lenovo's MBR / bootloader. However, after a search online I found Lenovo only provides the MBR fix for windows XP and 2000, not 7.
Any suggestions?

Fixing the MBR shouldn't alter the functionality of programs, unless you've changed the drive letter somehow.
Reinstalling R&R within Windows should get it to work again, though.
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