This article might be of interest to you, looks like a similar problem and layout...
From custom pc. http://www.custompc.co.uk/blogs/mremulator/2008/12/11/overclocked-orange/
(hit ctrl-f and search for dremmel to find where the pictures are for this article.)
I thought I’d better quickly offer up my X-fi Fatal1ty Titanium to the top PCI-E slot before the case arrived, as expected the NB heatsink blocks the card.
However, all I have to do is remove 4x fins with a dremmel and it will fit perfectly.
4x fins removed & filed down
X-Fi fits nicely now