?!?!?!?!
You shouldn't have to cut down pistons. So this isn't a typo, you have almost a half inch of protrusion? If I'm not mistaken it's suppose to be .014 to .031. I don't understand how you can be at .4... Almost sounds like you have a factory defect with your pistons to have that much protrusion.
As for valve relief, that depends on the cam. I think I went with a stock deck height and .036 valve relief.