You can see in the second picture how I cut out an opening in the first box. This is where your little person will be as he/she "rides" the train, so cut it to fit. Cut the flaps off the bottom part of the first box. Your child's feet will come out the bottom.
The next step is to cut out the train wheels. I used the third box and a salad plate as a template. I also cut a long strip to connect the wheels. I'm not sure what this is called, but you see it on the real Thomas' wheels :).
The final step in the contruction phase is to make Thomas' head and smokestack. In my research, I saw that many people used premade containers like oatmeal canisters for the head. I thought this looked too small for the scale of the train, but you may be able to find a bigger cylinder. I decided to make my own. I used a bowl to trace and cut out a circle, and then I used a strip of cardboard to wrap around the circle (I also cut a slightly smaller circle to fit inside the cylinder a few inches down to stabilize it). Use the hot glue to secure.
Trace around the cylinder on the front of the train, and use an X-acto knife to cut out the circle. Shove the cylinder through the circle. You want a tight fit. Then use packing tape to secure the cylinder on the inside of the train. Follow the same steps for the smokestack. I used a papertowel roll cut in half. The only difference from the head is that I secured the smokestack on the inside by cutting the tube lenth-wise several times on the inside of the train and folding those pieces outward. I taped them to the inside of the train.
Now you have your Thomas costume constructed. At this point I used a ruler and sketched out where I wanted the lines to go. Do this with a light hand. Some of my lines and color notes were hard to cover with paint later.
When the paint goes on is when this bunch of cardboard starts looking like Thomas, so stay tuned...