Well I resanded my part with 1500.  Got a nice smooth matte finish.  And started the clearcoat.

Sounds like you have pin-holes in the laminate.  These are microscopic holes in the weave of the fabric that the clearcoat wont fill if sprayed.  Flat it back as you have done previously.  Dilute some clearcoat twice what you would do for spraying.  Brush this on and work it into the surface with the brush as much as you can.  Let it go off fully then repeat.  Now spray it, should be fine then.

I took it back and there are a few thin spots now.  So I'm going to add another couple layers of resin and resand. Maybe that'll put me in a better place.