Keep the answers coming, someone will say the magic word.
With the W engine having the flat head, the combustion chamber is in the cylinder. The piston to head clearance area is the quench pad on the 09 piston. It's the shape of the piston past that quench/squish pad that provides the combustion chamber volume. That's where the W gets its compression number. That's what makes the 409 the engine it is and makes it different from all other engines with their combustion chamber in the head. So, piston and gasket thickness determine quench, piston shape determines compression. I hope I made that clear, it's a little early in the morning and I haven't had my coffee yet!
You're going to have to have your machine measure and square the block.The bluepgo nt spec.for the distance from the crank centerline is 9.600.Once that's done,you can supply the piston maker with the spec's and they can go from there.These old blocks can vary on the deck surfaces from front to rear,as well as be different from side to side,by quite a bit.The piston maker will need to know the deck height,stroke you're planning to use,and the length of the rod that you're going to use.On a stock 409,the rod length is 6.09,the big block Chevy rod is 6.135[much better rod],and the best choice is a 6.385 length rod for several reasons.
Since you already have the pistons,mock the engine up using the crank,and one piston and rod assembly.Measure the distance from the deck to the piston top at it's highest point at maximum rock.Do this on all four corners of the block.You may have the piston deeper from one side to the other as well as one end of the other.Since you'll want the piston to protrude a little[Jack likes .002,Aubrey likes.004],you can then determine how much to mill from the block.If your machinest can't understand Jack,he doesn't know W engines! Find one who does,regardless of distance.The last thing you need is someone screwing up these hard to find,expensive blocks.