The ignition switch and the alternator wires are not fused, they simply attach to the buss bar.

There is a terminal for the ignition switch coil on the fuse box, which is protected by a 20 amp fuse. Should I attach the brown wire going from the ignition switch out to the coil, or should I just leave it as is?

To answer a prior question, yes, the splice from the alternator wire is removed.