Some progress. I have another fan controller this time and it works properly. I might get some thermistors for it since it supports 4 of them. But I don't need them. I got the custom fan I made installed and the heatsinks on the voodoos. Surprisingly they don't even get warm. Also I don't experience any of the problems other people have with running voodoo2 on fast cpu. Them getting hot and bugging out and what not. This Thing goes balls to the wall and its more stable than any of my other rigs it seems like.
The 6800gt on the other hand is a little space heater all on its own. Even after repasting it and finding the right thinkness thermal pads it still idles at 60c and under load 70c on 98se. This is a factory overclocked model however and from what I gather the 71xx drivers do run hotter especially under 9x, from everything I've seen this is normal.
Also I ran some 3dmark 99 bench on the voodoo and verified that ya it's in line with a V3 3000, maybe slightly faster on this rig. I can post them up but they are what you would expect to see.
Lastly I pulled out the creative cancer card, and replaced it with a SQ2500. I'm looked for another non creative pci card to pair it with if anyone have suggestions. Preferable something with better EAX that the a3d.