I don't think there's much danger of causing the valves to strike the head, the valve lift is about .312" if I remember right, and the combustion chamber in the head is around .572" deep. There is a possibility of "shrouding" the valves by reducing the space between them and the "roof" of the chamber, thereby reducing breathing ability. This was always a problem with the Flathead Ford V8's. But there again, we've got plenty of room above the valve that the Ford didn't have, plus the valves are recessed into the top of the block in the Ford, and the Go-Devil valves are above the deck. So, this may be an issue with the Go-Devil, and may not. I don't know.
The problem that I see, is that there is a flat place on the Go-Devil head directly over the top of the piston. The iron is not real thick there, and whatever amount you plane off of the head, will reduce the thickness of that part of the chamber. BW