Sounds like you have GeeBee floats, the hobby shop should have installed a sheet metal srew in each hole in the top of the floats before they gave it to you. They come with the floats and work well to seal the stock opening. Now that you have unlarged the hole you have to figure a good way to seal it. I would try Goop and see how it works. With the hole sealed you should never have to worry about water getting in unless you run around on land and wear out the bottom of the step(I've done it).

I would not try filling the floats with foam, it'll make them heavy and the water will still get in and then be harder to get out. The GeeBee floats are good, try to fix the problem before you go replacing them.

As far as pulling to the left. The water rudder you have shouldn't be doing it unless they istalled it in a way that causes a whole lot of drag. An easy cure would be to take it of and see if it pulls with out it. Unless it's windy you can fly, actually taxi, without the water rudder. More likely the floats are not parallel to each other both looking down from the top of the plane and from the side. A good and easy way to check the parallelism from the top is to set the plane on a tile floor and use the lines in the floor against the centerline of the fuse and the center of each float. The tip of each float should also protrude the same distance from the front of the plane.

After you check these items out let us know how it works.