Well the things that come to mind are a vacuum leak somewhere. It could also be that you still have a coolant leak somewhere that is not allowing the system to pressurize completely.

What concerns me more, and I dont know what the possibility of it would be, is that maybe you have a blown head gasket or maybe one of the heads warped some from that temperature. Doesnt seem likely, but given all you have done I dont know I would rule it out at this point.