If you're sked under 24 hrs at YVR then you are clean. Not only does it not count as a stopover, since it is a connection, you only need to use 1 SE certificate to upgrade from origin to dest.

The agent at YYZ will be unlikely to be able to issue the connecting boarding pass. Ask her to insert a remark in the PNR that the U/G has been lifted at YYZ. If you have a paper ticket, ask her to write it on the face of the ticket.