The Manuka Honey doesn't smell :) But really, the oil absolutely stinks, and the smell doesn't wear off during the day.
I leave the honey on my scalp, under a hat, so it's there for a long time. I also have a problem with the bacteria on my face, and regularly leave it on my face overnight.
Regarding totally getting rid of the infection from your body.......
In may case (I don't know about yours or anybody else), I've been told by 2 derms that I am a carrier of the infection/bacteria, and there is no way to get rid of it 100%. They said that the bacteria live in colonies under the skin, and sometimes in the nose. Although Antibiotics may lesson the effects, and even make the symptoms disappear or a long time, I will always be a carrier (barring discovery of a new medicine).
This also makes me believe that using blue light (or other light) therapy for the infection may well clear the infection on the surface, and improve skin condition, but the underlying infection will continue to be present in the body.
But I stress....this is only what my derms said to me, it may not apply to everybody.
Please don't worry about your new small spots. I got those as well, but they get smaller and smaller and gradually stop. I guess that as we are shaving, we are still spreading infection to other areas of the scalp, there is no way around this. Fortunately, as we have shaved our scalp, the infection can't be as strong as before, hence the new smaller spots.