I was starting to worry that you were going to copy route round that lot for a while.
I find that once a layer of varnish has been applied things will look a whole lot better, you wont really notice the filled bits as the layers vary in colour. I would go with Jasons advice and if you really aren't happy at the end spray it. Rustins plastic floor coating is nice on birch faced ply and really toughens up what is a quite soft board, put the first coat on really thin so that it penetrates well and add thin coats to build up a good finish. You can do this quick with RPC as it dries in quarter of an hour in the warm, It does stink though.
Simon