I'm on my phone but I'll try to answer your questions as best as I can (I will just clarify when I get home later on my computer)
1. Not sure about MMR vaccine, it was not required for me. The doctor who did your medical should tell you everything you need. I'm not sure if they check your blood titers for vaccines on the test since I never saw my results
2. I'll have to look this up again but I don't think you need to since the 'dependents' they are referring to are children/spouses that need to be sponsored and since your daughter is already a Canadian citizen, it doesn't apply to her. Again I'm not sure about this, best to call the CIC call centre to ask them.
3. I suggest writing N/A on all the questions that are not applicable to you so CIC will know for sure that you read all the questions and you didnt just forget/overlook some items. I just wrote it with a pen after I printed it.
4. I didn't write a cover letter but we each wrote a personal statement as part of the 'proof of ongoing relationship'. There were some who didn't write anything and they were still approved. In my case, it made me feel at ease having the personal statement, it provided a more personal touch to your application and gives you a chance to explain anything that you think the application questions didnt cover. Doesn't have to be novel length, ours was just one page.
5. As far as I know, you only need 2 checklists - the one for the sponsor documents and the one for the principal applicant. Both of them have to be checked for all the requirements or written N/A if it doesn't apply to you. Don't send a blank one!
Good luck on your application! I have a feeling applicants these year will go through faster than last year's with all the changes CIC is doing