Block has many places small amount of rust can linger, battled this issue, more than once.. mine wld work fine for a while after flushing the heater core, then start doing it again.. so I was fed up.. I removed the thermostat housing, water pump, radiator (which is new) and flushed the block, heater core, and rad.. and now it works like a dream..
it only takes a small amount to clog the heater core, pull both lines, flush it (heater core) with water hose in both directions, cpl minutes on each side.. you should be good to go..

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1999 MAZDA 2500SE, 2.5L 4-clanger, 5 speed, Green n slow. Rangers as daily drivers since 1988.
ASE Certified Mechanic, Builder of Show Destroying Protouring and Classic cars..