Have been tearing down and fixing things since young, have good experience with electronics and mechanics.
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Answer to "Can you buy replacement black rubber bands for wheels?"There are companies that sell large sized rubber bands. Perhaps something from a camping shop? http://www.rubberband.com/about-us/rubber-bands-size-chart
Answer to "buy replacement track piece"It should be possible to make some straight track pieces from wood. Curved pieces might be a bit more challenging.
Answer to "Why is the train not moving"I wrote the strip down guide the train I had did not work at all. My two main issues were: 1) the lever controlling the direction had been pushed beyond it's limit. Once I'd taken apart the steering wheel it was possible to get in to change that back. 2) the switch for the power was broken, this was fixed by reversing it around using one of the spare contacts.
Answer to "Replacement Charger for old Thomas ride on train and tracks"You could always take the battery out and use a car/motorbike charger instead.