The reason it's backdating and not modifying is because the show's Thomas changed quite a bit from Season 5 to Thomas & The Magic Railroad. Since my favorite season is season 3, I will make my model represent that more accurately. I have done the first modification today of swapping Thomas's original wheels with smaller ones, which are accurate for at least the first 3 seasons of the show. Thomas later gained larger wheels for his Magic Railroad rebuild.

I did have to repaint the wheels from their original color (black) to blue. I found Vallejo's Deep Sky Blue to be a fairly close match to the blue of the model. This also fixed another issue with Bachmann's model of Thomas: the overall height of the model. Thomas's cab in the show is supposed to be close to the height of the vans used in the show. The Bachmann model's bunker goes to the top of the vans (I forgot to take a before picture), but it is now closer to the correct height. While it's not perfect it's something I can live with.

Moving on with height issues, the Bachmann model's running board was also higher than it was on the show when compared to Annie and Clarabel and the trucks. This is also now corrected, however highlights a few other problems with the Bachmann model (will get to that later).

Now onto the issues brought with the change. This exaggerates how far down the front bufferbeam extends, which makes the buffers and coupling sit too low. It needs to have a couple of millimeters removed from the bottom and the buffers moved to the centerline of the modified bufferbeam. I may use one of Duck's coupling hooks instead of the oversized one currently on Thomas's bufferbeam or I will get scale ones to use once that is done. Moving on to the rear bufferbeam, it shows that the buffers are sitting too high. In the first seasons of the show, wagon (and Annie's front) bufferbeams were lowered to Thomas's buffer height. Later on, Thomas's buffers were raised instead so that wagons didn't need to be modified to be used with him.
This modification also introduced a couple of operational issues. The knuckle coupling that I put on the model is now too low to be used, so I will need to cut it out to correct it, although he won't have a rear dummy coupling anymore (I will trade operation for some accuracy). The pickups are also now in the wrong place. Although they still work, I fear that they will break with extended use. One good thing about that though, is that it will force me to use a soldering iron to fix them, which in turn will allow me to carry on with the modifications. Most of them deal with the running board, which I would prefer to remove from the model before I start cutting it up too much (the wires for the pickups fun through small holes in the board, keeping anyone without a soldering iron from easily making modifications.)
Other modifications to be made include:
-Rivets (the close-up model had them)
-Changing the front lamp's shape
-Moving the rear lamp down
-Rear lining
-A new face
-Guard irons on the rear Windows
-Possibly opening the cab
-Adding other various painted details
*Example of close-up model rivets:

Thank you for taking the time to read this. More posts will be made as things are completed. I hope you found this interesting.
-TrainMan2001