PR has a portal but it's only required if you are leaving the airport. If you are simply picking up your checked bags and taking them to the InterCaribbean counter to recheck them, you are not required to fill out the portal. After baggage claim, there are national guard troops checking for the portal approval. You just show them your connecting information and they will direct you back upstairs to the ticket counters. My suggestion is to have your InterCaribbean flight information printed off so it's easier to show them.

Not sure about immigration/customs. I would assume you still pre-clear in Toronto. If not, there is a very large, efficient immigration area in San Juan. According to the US CBP website, the pre-clearance is still active in Toronto. I'm sure you know, leave yourself a lot of time in Toronto unless you have a Nexus card.