on a 4AG with flat-top pistons, the crown usually sits about 030" below the deck surface. there is no way you want them protruding, especially on an old engine that has head shaved several times, otherwise your compression ratio will be too high. You can correct it with a thicker head gasket, but its not ideal. what we often do for such cases, is machine a squish ring on the piston crown, say take 020" off a small ring around the outside. .
To give you specific advice, I need the exact data on pistons, head chamber volume etc.
terry
