I’m a Canadian student, and here’s what I know:
Your whole credit summary will be sent to all of these schools. That means all of your marks from grade 9-12. However, this is just meant to review and ensure that you have completed all of the graduation requirements to attend the school.
What really matters are your grade 12 marks. YOU get to choose your top 6. Grade 12 English + any course requirements for the program must be included in this, but the remaining spots can be filled in by your top marks, or most related courses. For Canadian schools, the average in your top 6 is what matters.
The marks that you send in when you apply will be your gr 12 semester 1 midterms. They will then receive your final marks for these courses before accepting you. They will understand if you haven’t completed certain courses in your top 6 yet, if they fall in the following semester.
The only time that they would consider your grade 11 marks is for early consideration.
That being said, there are rumours that Waterloo does look at your gr 11 marks, so be aware of that. Although I personally suspect that this may not be true.
Don’t bother redoing functions. It is clear that you understand its concepts from your Advanced functions mark. The AO should recognize this. However, writing a justification for the low mark and sending it to the AO wouldn’t hurt, as the above commenter stated.
I’m not sure if you’re a Canadian student, but if you are, isn’t this information given to you at school? If not, it really should be.
Based solely off your grade 12 marks, I think that your chances of being admitted is pretty average. There will definitely be applicants with better academics. Have you done any of the Waterloo math contests (and scored well)? This will look good on your application.
Unfortunately, most science programs in Canada don’t weigh extracurriculars as heavily, but your ECs would still be a good way to make your application stand out.
Good luck!