The cleanest way to do it would be to, as Byrd suggests, find out the relevant pins on the edge connector, make up a small card to go in the slot, and break that out to a VGA port on the back panel. A DIL header might be handy for patching sense lines connections and diodes. You could probably bodge something up on stripboard pretty easily. Then you just have to make sure your card goes in the right position in the slot and stays there.
Come to think of it, that last problem would be fixed by using a dead 5xxx motherboard, cutting off the whole edge connector section, and soldering leads to the edge connector traces or nearby pads.
Then you just need a way of tricking the analog board into powering up.
This would be reversible, as you could pull your board out and replace it with a 5xxx series motherboard any time.
If anyone out on the web someplace has done a 5xxx ATX/Mini-ITX mod, they probably have all the necessary clues.