You can leave the coaming and strip around it if you overlap the new glass over the old. However you may not need to completely refinish. Can you post a pic? Before doing the whole boat I would sand down carefully to where you almost get to the weave and then wet with alcohol to see if the cloudiness is still there. If not then sand to 400 grit and put a fresh layer of epoxy. It may just be in the fill coat or even the varnish and you might get lucky. I had it happen once and it worked for me.