Re: New Cylinder is taller; ports bigger
1mm to 1.5mm makes a big difference in compression. Before you put any labor into decking the cylinder or milling the head, check for obvious problems in port timing. With the piston at bottom, the transfer ports should be fully exposed and the bottom of the exhaust port should be flush with the top edge of the piston. If the ports are below the piston, don't waste your time.
You may be able to get back some of that 1mm by using thinner cylinder and head gaskets (beer cans are a good source of thin gasket material).
Either way, just make sure that you are leaving about 1mm of space between the piston and head at TDC when you're done.