Progressing well Andy.
Was the water pump leaking, looking at the condition of the O ring?
It may be a good idea to back flush the radiator with hoses off, in case any of that brown water contains sludge blocking the core tubes.
When surfaces are all clean it will be interesting to see with a straight edge the condition of the cylinder block and head.
I assume piston heights are all the same with no discrepancies re earlier concerns? Easier to check now head off.
It always surprises me that after much use, it is still possible to see the boring and honing "cross hatch" markings down the bores from new.
A little messy, but I often put an equal amount of oil on top of all pistons as a check to see if one drains away earlier overnight indicating a poor piston seal. It does involve cleaning it out before reassembly, but can be a useful check.
That process can also be used as a quick check with manifolds off and old spark plugs replaced using petrol or thin oil to check valve sealing if not being removed, as a poor one will leak into manifolds. Though I assume with yours you are overhauling the cylinder head anyway.
If replacing head bolts I find one ground on a grind stone with three flutes after wire brushing any sharp edges acts a a suitable thread tap to clean bolt holes.