A wiring diagram will be helpful in figuring out where those wires go. When you say 'little loops' do you mean that the wires are terminated with ring-lugs? My guess, is that they go to the coils, in the magneto. Color code on the wiring diagram will tell you which coils, etc.
In case you don't know this (forgive me if you do) to 'terminate' a wire, means to attach something to the end of it. That thing is usually a 'lug', and there are four common lug styles - 'spade', 'forked', 'bullet' and 'ring'.
The spade and bullet styles have interconnecting male & female types, the others do not, as they are intended to be secured by a screw or bolt.
As for the brakes, search the forums.. there is a Moped Dictionary thread, and I made an entry on brakes that covers some common issues. There are other good threads on brakes as well.