Don't modify the head gaskets I drill several .125 holes in the thermosat flange to let any air out of the cooling system when filling it initially, I've seen more than one new motor act just like yours did because they weren't full of coolant As far as tightening the studs more than finger tight They don't need it, you can try inserting a short handle allen head wrench and snug them slighty, if that will make you feel better
AKA, you can also try filling the block through the top radiator hose with the drilled thermostat to make sure it fills all the way up I have filled them up and then squeezed the top radiator hose to make sure water squirts out of it into the radiator on radiators that the upper outlet is in line with the radiator cap fitting You do know that Murphy hates hot rodders, correct