I need a good recipe for a heavy cake that will work well for a 3D thomas the train cake. I am attempting to cover this cake with fondant for my son's 2nd b-day. Any helpful ideas with that will also be great!

Try the White Almond Sour Cream cake from this site. It's in the recipes section and can be made in chocolate and many other flavours if you don't want a white cake.

I did a Thomas cake not that long ago, it's in my pics. It was a 3D cake and I just used the 3 D train pan not the actual Thomas pan. I ended up making mine out of pound cake. It made it sturdy and a whole lot easier to cut. The kids loved it and we served a strawberry compote with it. I however did not cover mine in fondant, I used a great crusting BC and RI
Good Luck