You could use a numbered list:
The project answered two very important questions:
- How does Ontario's mineral tax rate compare with those of other provinces and territories?
- What are the reasons, if any, that justify revising Ontario's mineral tax rate?
In that form, there is no need for the leading and.
The numbered list (or "vertical list") is an acceptable format in Chicago, and is further discussed at this web page, where they use a similar construction as an example:
Many writers to The Chicago Manual of Style Online Q&A ask how to format lists, and two questions are especially popular:
- Should items begin with a capital letter?
- Should items end with any punctuation?
If you really wanted to keep the and for some reason, I'd recommend using only one question mark:
The project answered two very important questions: How does Ontario's mineral tax rate compare with those of other provinces and territories, and what are the reasons, if any, that justify revising Ontario's mineral tax rate?