I'm in the process of placing the rad vertical instead of horizontal. Having the rad at the top was making things too difficult: The system was too hard to bleed and temps were not what they could be. I would rather loose all my 3.5" bays than my 5.25" ones. I lost two 5.25" bays when I mounted the rad at the top, which caused me to lose my fan controller and my DVD drive.
Mounting it vertically is going to make it a lot easier for a number of reasons. First off, you'll be able to bleed the system much better and quicker than with the rad mounted horizontally.
Secondly, It'll be able to silence the HDDs by using elastic bands that are stretched between the 5.25" bays. There was an article here on OCforums but I can't remember where it was. Can anyone provide a link?
Additionally, temps will improve. You'll have enough room to install a shroud; something that I couldn't do with the rad mounted at the top.
Finally, the noise level will drop due to the absence of the 80mm fans and the shroud.
Hope that helps.