[Occasionally6]

The engine manufacturer will specify how much material can safely be removed from the cylinder head. That will take into account valve to piston clearance and knock resistance. Often there will be a mark cast into the head for reference. You might use that as an initial guide.

They will also usually specify how much the combustion chamber volume is reduced per amount of material removed. Maybe ask at a shop that does the machining work what those values are. (I doubt it's in Haynes, but you never know...)

As a pretty close approximation of the latter, if you trace the outline of the chamber, at the head sealing surface, onto graph paper and count the squares you can determine the area of the chamber. Multiplying that by the amount you propose to machine off the head will give you close to the amount of volume change.

You will also have to include the thickness of the (compressed) head gasket in your compression ratio and clearance calculations.

When checking the clearance, take into account the effect of the VVT (check with the VVT in retarded and advanced positions) as that may alter how much is available. The rods will stretch with rpm and the valves may not exactly follow the cam (although they should) so there will need to be some (extra) clearance.

Combustion chamber volume may be measured (with the head off the engine) by sealing the valves with grease and measuring the volume of a fluid like kerosene it takes to fill the chamber. It is usual to use a pipette to measure the volume and place a sheet of glass or Perspex across the (levelled) head sealing surface so as to indicate clearly when the chamber is filled.

You might get an initial value by using the nominal compression ratio and swept volume (capacity) per cylinder and calculation to get the chamber volume.

The CR of factory engines do have to allow for such things as variable fuel quality, sketchy maintenance, oil burning with wear and Carbon build up in the chamber, so you can push it a little higher if you avoid those things. To be safe, you might just go to the limit of the factory service specs (as outlined above).

Machining the head or altering the head gasket thickness will alter (retard) the cam timing by bringing the cam sprocket closer to the crank while leaving the length of the belt on the tension side the same length.

An over bore (required with the new pistons?) will increase the swept volume and the CR even if the head is not changed.

CR is calculated by:

{Swept Volume (= bore^2 X pi/4 x stroke) + Head Gasket Volume (= bore^2 x pi/4 x gasket thickness) + Combustion Chamber Volume + (or minus) Piston Dish (or hump}/{Head Gasket Volume + Combustion Chamber Volume + (or minus) Piston Dish (or hump)}.

If you want to get really serious, software like Desk Top Dynos will allow you to build virtual engines. The basic program is reasonably priced. (Cheaper than rectifying something that doesn't work.)