i'm guessing by now you already know where you went wrong. first off, why so loose on the skirts? even a 4.5 bore Diamond piston usually only calls for .0055 wall clearance. what size bore is yours?
always measure piston rock from cam side to exhaust side without rings. what's the deal with having .004 difference in deck height, is that those 300.00 dollar rpm rods or the crank stroke?
in any case, glad you didn't hurt anything. you could always put a .045 or .051 gasket in there and screw it back together. i wouldn't expect any real longevity from the rings, but your probably not too worried about that. go have some fun with it.