2. If she is denied a WHV on those grounds, will that be a black mark on a PR Spousal visa application, despite there being no financial requirement?
The applicant having no money is not a problem. The visa officer wants to know that the two of you can support yourselves in Canada, though, so having savings is good. If she is young and seems employable, most likely it won't be an issue.
3. If we get married and immediately apply for a PR Spousal visa, will that raise red flags with immigration, even if we can prove the longstanding nature of our relationship?
No, it is OK.
4. On the Spousal visa application it has questions relating to having an engagement/marriage ceremony. Both of us are atheists and short on money, so we don't want to have a wedding. Will this be a problem?
It depends on the culture you two are from. In Japan a small wedding or just a 'town hall' wedding should be fine, but visa officers do want to see that the marriage ceremony was an important event for you. So try to make it look special, even if it is not a big, lavish wedding. Wear good clothes, have photos of the occasion, maybe have a few close friends and her family there. Even just going out to a good restaurant for a meal with her family after will look better than nothing.
5. Does anyone have experience with traveling to Canada on a visitor visa, after having applied for a PR visa? Was it hard to get a Visitor Record?
She can come to Canada without a visa for 6 months (if they let her in), which can be extended.
6. If I apply for government education loans to pay for school, will this be considered defaulting on my financial responsibilities as a sponsor?
No, you can get a student loan. It is only welfare they don't allow. But if you have a wife, will you have a harder time getting a loan? The loan people may expect her to work to support you, and may expect her to earn an unrealistic amount for a new immigrant.