I would epoxy the dowels and also smear a little more epoxy of the exposed dowels t fuel-proof them after you sand them flush. I'd personally use as small a dowel as possible but if you have 5/16 on hand that will work.

How much of the ply got knocked out with the old blind nuts? You could just fill the area in with epoxy if it isn't too bad but the glass cloth will definitely make things nice and strong. If you use it, go ahead and put it out to the edges of the firewall and on to the fuse sides. This will help any possible future firewall problems.