Somehow the little black rubber thing that goes with the brake got folded over the silver round clip... I tried various tools (After my fingers etc hadn't proved useful) in trying to drag it back but it proved seemingly infeasible. So I cut the black thing, then tried to brake and it clicks as though this thing is needed for the brake to clip in.
What have I done wrong?
If the "noodle" doesn't clip in right and seems like it is sliding through the "noodle holder" when you apply the brakes, then you might have messed up the noodle holder when messing about with the boot. There should only be a small gap in the top, just wide enough for the cable to go through. If there is a larger gap, you can try squeezing it either with your fingers or pliers to make the gap smaller. I've fixed brakes this way before. I think if you have to do this too often, then the noodle holder might break from excessive bending, but if you only have to do it once, it should probably be safe. See the image below for terms you may not understand.
The 'black thing' is just a boot to keep dust and dirt out. Cutting it off will not have caused any problems with the brake. Is the noodle (The tube the cable goes though) sitting correctly in the hole on the brake caliper?
When you release the brake the noodle is probably sliding back a bit because you don't have the rubber boot to hold it in place. So then there is a gap and it clicks when you apply the brake again. Does the noodle slide back when you release the brake? You might be able to fix it by lubing the cable/noodle. I suspect you can go to a bike shop and get a new boot - that is what I would do. Or you might be able to use a tie strap or O ring to hold it in place.
