Thanks all, for the drain hole advice! I called the shop today and told them NOT to drill any drainage holes.
On another note, I am thinking about installing exhaust flappers in-place of the SuperTrapps. I have read the threads but it isn't real clear to me if I have to remove and shorten the stainless steel piping in the boat, or do I just cut off the threaded part of the SuperTrapp flange?