boss97,
Sadly thanks to years of underfunding and the resulting cutbacks caused by lack of funding, it's not possible to do what you want entirely by train.
In fact one can't even get from Chicago to Toronto by train, at least directly. You'd have to take the Lake Shore Limited, train #48, to Buffalo or perhaps even further east. Then transfer to the Maple Leaf, train #63, to reach Toronto.
As for Yellowstone, your only choices would be to either drive or perhaps catch a bus from Salt Lake City, which can be reached by train. I suppose you could also catch the Empire Builder, train #8 from Seattle to Havre Montana, then drive down to Yellowstone from there.
So your itinerary might end up looking something like this.
Amtrak Train #4, the Southwest Chief, from Newton to Chicago.
Amtrak Train #48, Lake Shore Limited, from Chicago to Buffalo.
Amtrak Train #63, Maple Leaf, from Buffalo to Toronto, overnight stay required.
VIA Rail Train #1, Canadian, from Toronto to Vancover.
Amtrak Train #517, Cascades, from Vancover to Seattle, overnight stay required.
Amtrak Train #11, Coast Starlight, from Seattle to Emeryville, California.
Amtrak Train #6, Califonia Zephyr, from Emeryville to Salt Lake City.
Rent a car to go to Yellowstone.
Then you could either return to Salt Lake City or head to Havre for your return to Chicago and eventually the Southwest Chief to Newton.