Be sure and measure the bore the head is set up for. You spacer plate will work fine to +- zero out the piston to top of cylinder. It sounds like you have a couple common issues, stock head that hasn't been chambered properly for the bore size and a sleeved cylinder. As you piston grows in over sizes you NEED to have the head opened up at some point to properly clear the piston or you can crush the ring lands. A sleeved cyli deer will have had the topof the cylinder trued to set the sleeve the same height as the casting.  If there were imperfections it could have had a lot taken off usually  a few thousandths is all you need but a bad cylinder ;can require much more.
Be sure to check the head.