Some other places where water could drain into the boot and you might find similar problems:
- the c pillar badges (rust develops around the two holes, then it can drain down into the same area. Will be worse if you've vinyl covered c pillars))
- the chrome strips that run around the c pillar window (more holes that will rust)
- the c pillar window seal itself
- the rear window seal
- the two drains in the boot lip, check for rust around them inside the boot
- the wiring loom that comes in through the LHS front of the boot, it's probably not sealed properly
- the mounting bolt holes for the rear bumper
- rear tail light seals
- the panel join under the rear tail lights
- check all the rubber bungs in the boot floor
- check for rust holes at the boot floor/ wheel arch join area (especially if holes for mud flaps have been drilled).
They're a few of the places I found my boot was leaking from!