[Stitch]

Could be due to something called 'solvent pop' , it can happen when you lay the paint on very heavy and/or the ambient temperature is too high at the time of spraying or not enough flash time between coats.
The paint skins over before all the thinners/reducer has had a chance to evaporate it then tries to push it's way through the skin causing small bubbles or pinholes to appear. Do the blems your getting look like this ? , fish eye looks like tiny craters and is usually caused by silicone contamination on the underlying surface .

As Jason says your remedial plan sounds good and you probably won't need to apply any more clear coat , make sure it's fully cured though before you wet sand.