i had a similar issue with my old skyline... misfiring and no compression on a couple of cylinders. gasket had gone on the water jackets allowing water to get into the combustion chamber. verified it by taking spark plugs out and cranking it over (water came out
).
since you have the head off get it done and pressure tested. Make sure you check the block for flatness and put it all back together with new gaskets and you should be right