Head is back together and installed with new bolts and a genuine head gasket. I spent a good hour doing the torque sequence and making sure the bolts had stabilised at each torque. Also wiped the block and heads clean about 10 times to make sure they were meticulously clean.
I've had the problematic water ports blocked off at the rear of the number 6 cylinder. I'm not concerned about this causing issues.
Rocker gear all cleaned up and installed. Will set the clearances tomorrow. Intake next, waiting on some gaskets for the oil cooler, then it's time to reinstall it into the patrol.