On the brakes, I suggest flushing and bleeding both front and back. See if that helps. If not, you may need to rebuild the master cylinders at least but with a 15 year old bike, a full brake job on both front and back (masters and calipers) may be in order. Being able to stop when you want is very important!!!
On the rough idle, that may be a bit subjective if you are coming off a Triumph and comparing the Harley to that. But if it is really running rough, then you may want to change out the plugs and even plug wires. Run some fuel system cleaner in it for a few tanks. See if that helps.
Cheers,
TQ