Sorry for getting all involved in this, but I am having some serious problems with what's going on here. The first thing I have to ask myself, is how did this problem (the piston being at least .040" proud of the cylinder) come about? There are only two ways I can think of that can cause this. The first is there's something funny going on with the crankshaft, rods and pistons. I would think this would be highly unlikely, which leaves my second choice, that the block has been decked excessively. Since no flathead ever left the factory with an ideal .050" quench, the decking must have been .060"-.080". Given the notorious thinness of flathead decks, I would be very wary of this block.
If any of you can come up with a flaw in my logic, I'd like to hear it so we can put the O/P's mind at ease. The way things stand now, I believe it is imperative to find out what the actual cause of this situation is and not just throw a "band-aid" (yes, that's what it is) of non-standard thick gaskets at it. I'd at least want to sonic check the deck to find the actual thickness.
This sounds like it's a high class, high buck build that deserves to done right, not finished with a patch. If someone else can tell me what's causing this, lets hear it. If this were my engine and my money, I know I'd sure like to be sure I know exactly what's going on.