I don't think you'll have any issues with the new style head. The missing two water holes don't move much coolant, the main ones are still there, just make sure you ensure you get the correct thickness head gasket, if you took a metal one off, put one back on, same if it was composite, top clearance is very important.
I work for a company that rebuilds diesels engines, we call the newer style head the B version, it has both styles of rocker cover holes so it's backwards compatible, the older style have the 4 studs in the middle to hold the rocker cover on, the newer ones have a rocker cover with bolts that go around the outside. This head also fits the 2403 (same bore size, but longer stroke) that i believe uses the later style rocker cover.
One thing to check before you put it on, is there is a grub screw in the thermostat housing mounting point, this seals the oil gallery, make sure it's tight or even remove it and put thread sealant on. Some came with grub screws, others have ball bearings pressed in, to ensure it doesn't pump oil into your cooling system.
Another note, if you do have a composite head gasket, ensure you re-tension it after 6-10 hrs of operation, they do compress, metal ones won't, they are set and forget.