[MikeK]

Your 0.125 overbore will not make it run hot. A rusty block is an insulated block and will be trouble. So are limed up radiator tubes. When the head comes off again you may have to go into the water jacket openings with a piece of speedo cable in an electric drill to really break up heavy crud accumulations in every nook and cranny. You should then run a Gano type coolant filter for a while in the upper rad hose.

Do as Tom says, run antifreeze. But first fix that cyl! Then after some light heat cycles and re-torques to seat the new gasket with just water in the block remove the rust by switching to Tom's vinegar method or use a commercial chelator like straight EDTA or buy one of the over the counter rust remover chelation elixirs like Rust 911 or Evaporust. Both the vinegar and the chelators will also clean out deposits in the radiator but will NOT open tubes it cannot flow through.

Clean out the Gano filter in the upper rad hose after the rust and radiator lime removal then go to antifreeze to take advantage of its pH buffers and anti corrosion properties. I ran 50/50 in my town sedan way back in 2008 at the Dallas world meet and, with a 160 stat in the upper hose, even though it was 99 or 100 every day my engine never went over 180, even when backed up in traffic.

Of course this all assumes you are not running with retarded timing, which will cook any engine in short order.