One approach - the one I used - was to get the block cleaned up and checked and minimum mill cut to square the deck. Measure again and work from there. Figure rod length, piston height, gasket options ect. If you/your shop can take it in stages, its easier to get nice result and less chance for oops.
That's exactly what I did above, and I was able to measure, order parts, and tell the machine shop exactly how much to mill to arrive at the exact deck height that I wanted with my gasket. If you measure before the machine shop mills it square, you will be off after they correct it.
