Sounds like your battery is weak. Some car alarms go off when the battery level drops because it thinks its being tampered with etc.
Re the water leak, it could be the windscreen leaking if its had one fitted. They usually join the two sealer beads in the middle (transmission tunnel area you mentioned). If it was leaking by the scuttle area/bulkhead then the carpet would be wet, and sometimes its too late when you realise that, the floor pan has a puddle under the carpet.
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