Being that the control panel is metal, unless you have a very different layout planned, I would suggest keeping the old panel and just drilling out the new holes. Even if they overlap some of the old holes the metal will still hold out. My machine was a Batman before it was MAME and it was a Bad Dudes before that. Very different layouts with new holes drilled. It didn't seem to cause a problem. Any extra holes can be covered by an overlay anyways.
Otherwise I would say cut a rectangular chunk out of the old one and bolt down (either on top or through the bottom) a new sheet of metal over the top portion to make new holes.