I don't do anything special...level ground, add antifreeze until the radiator stays full, start engine, add until full. Cap it, let it get to operating temp, shut it down, let it sit until cold, check fluid, top it off, then fill overflow to proper level and I'm done with it.
Losing a massive amount of coolant with a cap off I can't see. Obviously coolant expands, but not THAT much. Sure sounds like the block pressure is too high when it finally lets go. But theoretically that pump might be putting a lot more pressure into the block.
Which makes me wonder...were all the pumps you used higher performance, or were some stock? IIRC the stock thermostat opens AGAINST the flow, which I would imagine would be a problem if you are putting more than stock pressure/flow against it. You have no cooling problems with the t-stat out...
I assume you haven't talked with anyone like these guys?
http://www.stewartcomponents.com/Contact_Us.htm
They sell stuff, so I'd always be suspicious of what they have to say, but maybe they've run into this before, with their business being cooling and all...just hate to see you waste more time and money guessing at the problem. No one here has nailed it down obviously, and you've tested/swapped/reswapped about as much as I can think of!