First question:
Which year/model is this engine? The amount of machining for improved performance will vary a little, based on the model/year. The 72.2mm height suggests it is a K4/5 engine: those often have taller cylinders than the pre-1974 versions, which Honda did to reduce the octane requirement of those engines during the gas shortage of the later 1970s era. At that time, premium was almost impossible to find, and American Honda told this to Honda in 1973. The result was a drop in compression in the K4, very noticeable at the time, to allow them to run on Regular grade fuels. The cam duration was also shortened slightly, to improve the compression numbers and to preserve the same carbs in use: this, too, worked well. The most notable change became the top speed, which dropped on average to about 105 MPH (down from a more usual 120-ish top end), but they still toured well.
To remove this and improve the overall performance again, there are some tests you can do to determine your particular engine's needs. For one thing: place 2 of your new pistons (without rings is OK) on their rods on opposite sides of the engine (like #1 and #4 or #2 and #3) and place the bottom gasket on the cylinders, then drop them into place. Bring the pistons to TDC and measure the depth from the top of the cylinder deck to the top(s) of the pistons: this is the clearance was was added (or not) to those cylinders. The original engine design had 0.00" clearance here: only the head gasket (originally 0.8mm thick) comprised the clearance between the deck and the head. Often there is extra height here: it can be safely milled off now, especially due to the extra thickness of modern head gaskets.
In the head: the valve pockets were deepened by about 1mm, creating small dished pockets where they now reside. This, too, lowered the compression a bit on these heads by increasing the chamber volume about 0.2cc per chamber and reduced the intake charge in proportion (by slightly delaying the intake suction moments) so as to reduce overlap charge and its resulting MPG losses. This improved the burn rate and made cleaner sparkplugs, too. To discover how much you can safely mill off the head toward increasing compression, measure from the edges of the intake valves to the head's deck, and mill off only enough to preserve (at least) 1.5mm of distance between the piston domes and the edges of the intake valves to ensure valve clearance at redline speeds. If you plan on running the engine hard and at high RPM, consider switching the valve springs to the ones found in the earlier engines: they are a little stronger at closing them at high RPM. The K4 and later heads have progressive valve springs for less cam drag, but they do close the valves a little slower at high engine speeds.
Generally speaking: it is necessary to mill of between 0.010" and 0.020" from the cylinder deck to restore the sealing of the O-rings between the cylinders and head, due to the increased thickness of the modern head gaskets. If this isn't done at a minimum, the engine will leak oil from these passages: the situation is that Honda always spec'd the MINIMUM thickness of the O-ring that will fit in any given spot, using their original design tolerances, and their supplier's head gaskets: today all those gaskets are thicker. The depth of the pockets where these O-rings reside, with the chosen head gasket in place, must let those O-rings rise above the head gasket surface by 0.2-0.3mm to have it seal well. Since this same thickness also reduces compression, milling the cylinders will in turn lower the head chamber to the pistons to recover that lost pressure.
