DEcosse
If it's no Scottish it's CRAP!
... I suspect the other wires are possibly my indicators and I may have disconnected them in error....
You cannot 'disconnect' your turn signals at the alarm connector - again, those are just parallel outputs from the Alarm directly to the signals themselves (do not use the turn signal switch or relay); so if those wires are unconnected that is not a problem.
The only common factor in the signals and the brake light is the Fuse (and you will likely find horn does not work either)
Actually also off that same fuse #4 is pin 6 - the constant power supply for the alarm - so if you connected pin 6 to something then again, that would be cause for the fuse to blow (or it may have simply blown when the alarm module smoked)