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When the battery tray rusts into holes its very likely rainwater will spill into the drivers footwell. As you say the best way of repairing it would be something like fibre glass or use a bridging filler such a Fibre-Fill. It may also be worth having the alternator out put checked as overcharging can cause battery acid to be expelled causing corrosion.
If the starter motor responded to a sharp thump it sounds like either a duff connection or faulty starter solenoid
Currently in madnoel10's garage:
Honda Civic 1.4l