Ok the hole on the water pump is there so that when the seal starts leaking it comes out there and not onto the bearing of the pump , this means that although the pump will need replacing the bearing will not fail so quickly.
If your lucky its your pump, it needs replacing anyway if its leaking so do that first.
The other optiong is headgasket/porous block whch could be pressursing the cooling system which as a by product could also be forcing water out of the water pump hole.
the reason I think it is porous block rather than headgasket is that your headgaskets are quite new and should not have gone again already unless the person who did them is a monkey mechanic.
If thay havent gone again then it could be the dreaded porous block as you could replace headgaskets all day and it will never fix the slipped liner/porous block problem which I gather the 4.6's are worst for.
cheap Checks you can do are to take the stat out and see if it works ok with boiling water, or leave it out and see how its running without it. It seems your rad flow is ok if you have back flushes it ok and had a good flow. next chepest would be the water pump to swap and its leaking anyway.
Test wise you could get a garage to do a sniff test for hydrocarbons in the coolant but people have been saying on here they are non conclusive. Do you have much pressure left in the cooling system after it stands over night? that can indicate the bigger problems but mine has a little and has been good for a year even when worked hard off road in the heat.
Have you bled the system well after your drain and flushing, it can be hard to get all the air out , epecially with your vapouriser added to the system. You fill it and then run it with the cap off untill its up to temp and pusing the water out, then put cap on and let it cool and top up after.
Final bodge job before spending the big bucks would be to put some k-seal or ironite in andhope it works , if not it may be costly.
I hope this helps you a bit ,it not a good thing for man to have a broken v8!