I would pull the battery out and the plate it sits on. There is a vacuum hose under there that goes to the A/C blend door I believe. It could easily have been rotted out from the battery setting above it and could possible be a path for water to get into your passenger compartment.

Now that you have blown the drain lines out I would run water through them to be certain they drain properly and be sure the small rubber guard directly under the hinges is sitting in there properly.