Having cut up and inspected pretty much every cylinder head from Briggs and Strattons to very expensive F1 items for analysis I'd say make everything about 5mm thick, the deck faces 8mm on the heads, and 10mm on the blocks. The combustion chamber roof 8mm, but make sure you have ample coolant flow internally around the plug counterbore. This can be tricky in terms of making the coolant gallery core there so keep soluble ceramic inserts in mind and also cross drilling from the exhaust manifold side. Watch the areas where the valve guides will live as these will cool after the port roof walls and may cause hot tears - ideally your risers will sit ontop of these for directional solidification but may be impossible chop off once out of the sand. Make the bit where you bolt the sump pan to 25mm wide and 20mm high and dont spare the fillets - the pattern makers/CPS Layer'up'er guys will thank you in time. All of the above dimensions are pretty much the same for a 1L 50hp engine to a 950hp v10 F1 engine so I honestly think calculations are pointless at this point - I'm sure someone still does them, but pointless all the same - I think. As for coolant flow simulation, this is normally done with casting number one - sensors buried in near plugs and the engine ran - the headgasket coolant holes are then enlarged or decreased for more or less flow depending. Aluminium is a good conductor as is the coolant plus its going pretty fast so I don't think that's super science either from what Ive seen. If you dont have a head gasket for tuning the flow, then do what they do in F1 where they have very expensive flow and thermal sim packages - drill and drill again and fit flow restrictors where you need them.
As mentioned allow for core shift on the ports - the tighter you want the core prints, the more sand that will be scrubbed off when fitting cores - this will have to be flushed out into the risers or will cause you trouble. If you make them looser they will be easier fit, but may move or float until they contact core print registration.
If you are diecasting the blocks then you can go down to 4mm in most areas, but remember to use far less machining allowance since the strength of diecastings is mainly in the surface skin due to the chilling effect of the permanent steel mould. If you machine off too much of this chilled skin bad things will happen.
Brian,
(have put 200 heads + through a 40yr old power hacksaw and swore as many times more with mis-filled complex prototype CPS castings)