SLK3000 B here with 8800GTX. While the card kind of fits with the HDD rack in, the rack pushes up right against the card. I measured roughly prior to getting the card so got some brackets to mount the HHD's in 5.25 bays.
Case does look a lot more spacious now, but my hard drives are running a lot hotter - before they were sitting in the low 30's with a 120mm fan blowing right onto them, they are now sitting in the high 40's/low 50's.
So I might look at grinding a small bit of the HDD rack away with my dremel, and putting the HDD's back at the bottom.
Just in case anyone is interested, wou will likely only get 2 HDD's in the rack if you mod the rack to fit with the 8800gtx in, and they will need to be in the bottom 2 slots.