Hi, I think I read somewhere on here that's there's wiring for the clutch start operation somewhere near the pedal, worth checking that's OK.
Rain may have caused a temporary short to earth somewhere that happened for long enough to drain the battery, I would check your sunroof if you have one, if not, carefully check all door and boot seals are clean and secure, attention to detail here is paramount because the smallest bit of dirt on a seal can let water in.
Check your owners manual for the sunroof removal procedure, remove it and clean the seal if it is dirty or green.
A duff battery can cause bother too, have it load tested.
Just because a battery gives a 12v reading it doesn't mean it has enough power, it is how many amps it gives out when asked for power. Hence the term "cold cranking amps" - a rating which varies from battery to battery.
Though in this case I'd imagine it is not the battery that is a cause, just an effect.
Don't know why it said brakes, may be related to the short to earth somehow.
Oh yeah, it could be possible that the alarm can go off if the remote plip button isn't used, the alarm goes off on most cars if it was locked with the plip and opened with a key.
Daft I know....