Well, you know, heat does expand metal. I would assume that since adjustments are to be made at operating temps, that the clearance values take expansion into account. Maybe recheck right after it heats up/quiets down. Maybe make sure motor is staying relatively cool. No exhaust leaks or fan/radiator/water pump flow problems. Depends on what you see on the temp gauge. If temp gauge is accurate.
Noise, then no noise, then noise..... seems like a heat issue. Down hill, up hill, down hill or Intermittent water flow. Thermostat. Air bubbles. Failing pump. Oil flow