A quick check on your video card from the Gainward's website reveals the following information (located in the System Requirement towards the bottom): "Requires a vacant PCI slot adjacent to the AGP slot. This board occupies two slots: AGP and one PCI."
You may find your products website here: http://www.gainward.com/html/product/vg ... vi2-gs.htm
So, if this is true, then you won't be able to use that card in either Shuttle you were interested in. The problem is not length. Both Shuttles (if not all) will accomodate up to almost 9.5 inches in graphics card length. But the AGP slot is at the edge of the board near the case housing. So, the card can't be wide and and have a tall heatsink or other obstruction. It seems, in your case, it does. What does your current setup look like now? When the card is pluged in, does it clearly overlap the PCI slot next to it? If so, your out of luck.
As far as the fans go, you can't stick a 92mm inside the case without removing the fan housing all together. It's built exactly for 80mm. Even the outlet on the back is just big enough for that, with very little room for compromise.
...review on newegg said something about upgrading the fan to 92mm
I believe they mean to the outside, most likely using a 80mm-to-92mm adaptor (usually in a push-pull setup). This is quite popular in the SFF mod crowd. But putting one inside in replacement of the 80mm is really not practical.
Before you worry about that, let's get the video card situation figured out.