Loud ear splitting noise feedback after stretching wav file clips

To eliminate the problem at the source, try disabling 64-bit Double Precision Engine in preferences. I've had something like the problem you describe when stretching audio with 64-bit DP enabled.
 
To guard against high-level audio glitches, you can put any limiter plugin on the last bus before your main outs (preferably something with minimal latency like Concrete Limiter); I believe there are also 3rd-party plugins that are intended for this purpose. I often have a bus called "> Main Outs" after the Master for other purposes that would lend itself to this. When exporting, use Source = Master bus instead of Main Outs or Entire Mix to avoid having that bus affect the finished product.
 
All that said, if you have your monitoring system output level and project gain-staging set appropriately, even a continuous 0DB signal should not be painful, though 'surprising' your ears with a high-level transient when they are attuned to a lower level signal can still be unpleasant.