First of all Canadians don't need a visa and they had a waiver before the visa waiver program was invented. So, she won't have an I-94.
If she is planning on going back you should start simply with an I-130 and she can get a visa from abroad. OR if she wants to stay for at least 3 more months, you can concurrently file the I-130 and full adjustment package (I-485, I-765 and I-131). She won't be allowed to leave until getting advance parole through the I-131. If she travels abroad without advance parole, the adjustment is dead and she will have to get an immigrant visa in order to return.
She will get a conditional status for two years due to the newness of the marriage (it is less than two years old at time of greencard approval). That will require a follow-up I-751 within the 3 months preceeding the 2nd anniversary of the conditional greencard expiration. At that point you have to show that the marriage was and remains real (bona fide).
If you had gone to Canada and gotten married she could have come earlier with a K-3 visa and travelled back and forth with ease.
But according to the State Department website, that is no longer an option for her:
FROM travel.state.gov
Immigrant visa for a Spouse of a U.S. Citizen (IR1 or CR1) - An immigrant Petition for Alien Relative, Form I-130 is required.
Nonimmigrant visa for spouse (K-3) - It is important to note that application for the nonimmigrant visa for spouse (K-3) who married a U.S. citizen must be filed and the visa must be issued in the country where the marriage took place. After the visa process has been completed, and the visa is issued, the spouse can travel to the United States to wait for the processing of the immigrant visa case. Two petitions are required:
Petition for Alien Relative, Form 1-130; and
Petition for Alien Fiancé (e), Form I-129F
Advance Parole for K-3 or K-4 Family Members
Applicants presently in the United States in a K-3 or K-4 nonimmigrant classification may travel outside the United States and return using their nonimmigrant K-3 or K-4 nonimmigrant visa. The only time advance parole is necessary is if the K-3 or K-4 nonimmigrant status has expired and the applicant has an adjustment of status application that remains pending.
FROM uscis.gov:
Application Process
To obtain a K-3 or K-4 nonimmigrant visa, you (the U.S. citizen petitioner) must file two petitions with USCIS and apply for a visa from the U.S. Department of State.
Form I-130: File on behalf of your non-citizen spouse with the USCIS Service Center having jurisdiction over your place of residence. You will then receive a Form I-797, Notice of Action, indicating that USCIS has received the Form I-130.
Form I-129F, Petition for Alien Fiancé(e): File this after filing Form I-130 and include a copy of the I-797, on behalf of the non-citizen spouse and any children. Submit to the USCIS Service Center where the underlying Form I-130 petition is pending. There is no fee when filing a Form I-129F for a non-citizen spouse (K-3). If your non-citizen spouse has any minor children seeking K-4 nonimmigrant visas, they should be listed on the I-129F filed on your spouse’s behalf to facilitate the application process.
If approved, USCIS will forward the I-129F to the U.S. Department of State for consular processing.
The non-citizen spouse and any minor children will then need to apply to the U.S. Department of State for the K-3 or K-4 nonimmigrant visa.
Weigh your options carefully, you said she only took 3 weeks off from her job in Canada and apparently still has a home and posessions to deal with in Canada.
Good Luck,
