It appears to be IP2. However, you are not likely to get PPR unless all the aforementioned issues are resolved.
Perhaps, CIC wants all documents through MyCIC so that your actual application has reflection of it. Usually, additional docs are requested and uploaded through MyCIC account. If you see the additional doc upload slot in your MyCIC account then upload the requested docs ASAP. If you have already uploaded it make sure you have signed it and submitted it after the upload.
It's good that they have asked for explanation about the refused study permit. It gives you an opportunity to clarify this issue properly. Write a 'Letter of Explanation' (LOE) mentioning the technical issue that you faced during e-APR submission.
Upload the LOE on your MyCIC account, or as a Case Specific Inquiry at the CIC website mentioning your UCI and file number. You can also send them an email (to CPC Ottawa).