This is how I break a motor in. Others may do it differently, this is my routine. You need to fill the system fully with water/coolant. Start motor, 1800-2000 rpm for 20 minutes. If you suspect the system has air, have to get that sorted out, you really do need a full system. Sometimes the cooling system will not handle the kind of running with no air through the radiator needed for breakin so if that is the case and it sometimes is, I have a big box fan that I run through the radiator to get some air flowing. Sometimes, even that will not do it depending on the outside temp, like if I am breaking in a motor at the height of summer. So sometimes I have to run it 10 minutes, then let it cool down and do it another 10 minutes. Then I will generally let it cool and restart to idle and check timing and readjust carb if needed and then sort out whether I have an actual cooling issue. If it stays at 180-190 at idle then I am ok with that. The idea is to get the cam broken in and then deal with other issues after that.
I don’t know about 216 and 53 water pumps and whether one flows more then the other or has different flow characteristics. You might try getting a 235 pump on there instead of the 216 pump.
As for that plug at the back of the motor, yes, sometimes there Is sufficient sludge built up there not removed by the hot tank preventing water from draining from that spot. I would not read to much into that at the moment. When you get the pump off to put a 235 pump on (if they are different) you can look and see how much sedimentary junk is at the bottom.
