How did you check voltages at the boards? Make sure you are using ground on the boards to rule out faulty ground wire. Did the new boards come with all new ICs including new ROMs, or did you transfer ROM software from the old boards? If the boards are indeed new and working the first thing I would suspect is wiring. Start by isolating the MPU, no display boards, sound boards etc plugged in to make sure nothing else is dragging things down.
We can only *assume* the new boards actually work unless they can be tested in a working game...just something to keep in mind.