Something doesn't seem right, are you sure that it's on there correctly?
The only other thing that comes to mind, would it be possible to put bolts in the 4 outer surrounding holes in the valve cover and through gasket? The valve cover gasket just might pull just enough to keep the bolts in place and keep everything line up when you carefully reinstall the cover. The only thing that sucks is the amount of shit in the way.
I just swapped mine the other day, I did noticed that I used a small amount of RTV where the heads and the lower intake meet up. I imagine RTV could be used to fill in the gap, but it's possible you might still leak and it really sucks to clean up later. If anything drops behind the cover, it's going to eventally work it's way to the bottom of the pan and probably to the oil pick up tube screen (another reason why I wouldn't use a bunch of RTV).
Pete