I got a reply from Indy and they told me the location of the stand as well as how far to machine the heads. They said to machine the stands down until they are 0.500 inches above the tall head bolt counterbores.

I swung by the local circle track engine builder and he loaned me a Jesel shaft height checking tool. According to the tool I need to lower the shafts about 0.125 from where they are right now. That seems to agree with the number that Indy gave me so I think I'm closing in on it.

Here is a picture of the Jesel tool in action. The top of the valve tip is supposed to be flush with the top of the tool but in this picture you can tell that the valve tip is down in the hole a bit. So I need to mount the heads back up in the Bridgeport and mill the stands down some more.