First, I would sand the edges of each hole to a shallow angle. Also, sand the entire tray to get rid of all paint and glue residue.
You will need to add some thickness to the existing foam. Use some rigid sheet type foam and just spot-glue it on.
Or, use expanding foam. Pour a little on top of the surface, let it expand, and then sand to desired thickness.
For the sides, just tip the ski over to where the foam surface is horizontal.
Then glass over it, at least 4 layers of biax. Start out with a piece that's only a bit larger than the hole, then get bigger.