I’m with STW, I reckon you may have a crack in the head / barrel
I know you swapped the head for another but they could both be duds, stranger things have happened.
Cracks can be hard to see with the eye because they sometimes only open up with heat.
There are too many pages to look back through on this but I thought you said you had checked the water flow? With some clear hoses or something.
The recess in the pump case that is filled in is pretty minor as the outer cover still should have a good open area.
Have you had the motor running at your workshop with the cap off?
As well as watching for flow if the water settles down you can look for bubbles in the water, If there are any bubbles then they could be from combustion gases.
I think there is some testing gear that can check for gases, I think someone already mentioned it
You should talk to some car engine reconditioners about getting the head crack tested, they would deal with this quite a bit whereas motorcycle mechanics would deal with it rarely.
I reckon you need to get it tested properly just so you can at least rule it out.
Compare the cost of getting it tested to the cost of buying more head gaskets.
You can even buy crack testing spray cans from industrial type hardware stores.
I use it on odd jobs.