I did roughly the same trip last fall. I went Frankfurt - Leipzig - Berlin - Prague - Vienna - Munich - Stuttgart - Frankfurt (with day trip to Cologne).
Definitely go to Berlin too. It's a great city with interesting 20th Century history.
I bought a Eurail pass for the trains. They only sell it to non-Europeans, so order it before you leave Canada.
For hotels, I booked primarily with Hotwire and looked for 3.5-4 star hotels that were central to the city. Doing that, I got decent prices on most places, and everything was within walking distance of a U-Bahn or S-Bahn station and/or the city centre.
I'm as German looking as you can get, so I can't really comment on the racism. I didn't notice anything blatant, but I wasn't looking for it either.
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