I had the same problem with my set up.
I recently purchased an Asus u3s6 pcie card, and installed it. Afterwards, I tried to reinstall windows, but after putting the installation disc into my dvd drive, it does not boot up. I then removed the pcie card and tried the installation again and it finally booted.
In your case, you could try to remove all the components that are not necessary, ie. the blue-ray drive, sound cards, etc.
Hope that helps.
edit: Whoops. You figured it out while I was typing.