Aah yup, re-reading your post it makes sense that way,
It does look like you may have issues, unless an owner/builder can put in otherwise
I reckon your options are
try it, hope it fits
if it doesn't, trim the fan body or nb fins till it does
failing that Zigmatek coolers look to have better height clearance although you'd have to research them to find a 'good' one and I also saw this wierd beastie on the Egg http://www.newegg.com/Product/Product.aspx?Item=N82E16835220033&cm_re=775_cooler-_-35-220-033-_-Product
hope that helps a bit?