I have a valid US visa, no required Visa for Japan but my nationality requires a transit visa for Canada. I will be flying USA <-> Japan onboard Air Canada with layovers in Toronto for 1.30 each way. There will be 11 days between the two layovers/legs. My question is: do I need 2 separate transit visas for each leg? Should I opt for a tourist visa for the time in between (probably not?). Does the US-bound leg have some form of exemption from Candian transit visa?
You do not need two separate transit visas. When you apply for your transit visa, provide your entire itinerary, noting that you hope to transit twice through Toronto. If the visa is approved, they will give you at least a dual-entry transit visa.
Applying for a tourist visa for the time you're in Japan would only confuse matters. Since you won't be in Canada for that time, it would not be right to ask for a Canadian visa, and your application would likely be refused.
As to the US leg not requiring a visa, there's no such exemption. US permanent residents are exempt from the Canadian visa requirement, but since you hold a US visa you must not be a US permanent resident. Some European countries have an exemption for airport transit visas when the traveler holds a valid US visa, but Canada does not have a similar policy.