Welcome to the forums! I'd suggest visiting a few junkyards in your area if there's any available, as that's probably the most likely place you are going to find the plastic panel near the rear quarter panel.
As for the leaking trunk, I'd recommend getting in the back while someone wets the back end of the car with a garden hose or watering can. There's a lot of space and light in a wagon, so it shouldn't be too hard to pin-point where the water is entering from. A flash light would come in handy too. Chances are that the water is entering through the torn piece of rubber that you mentioned, but there's only one sure fire way to find out.
The 6th Gen Corolla forum here is jam-packed full of useful information, so you're bound to learn lots of interesting things. It might also pay to have a search in there to see if there are any areas where water is prone to leaking into the trunk. Damaged tail light seals are another common place for water to enter.
Best of luck, and enjoy yourself here at Toyota Nation!