Another possibility, although I think this wold have been resolved after you took it apart for the headset maintenance, is that the stem is creaking. Make sure the pinch bolt and all of the stem shaft points that fit within the fork have a thin layer of grease on them. Also grease the pinch bolt/nut for the handlebars. The grease allows it to tighten up more and not rust when you sweat all over it.
Being aluminum it could also be the seat post creaking in the frame (maybe even the seat) because sounds travel on a alu. bike more so than any other bikes I've owned. You could remove it and make sure that it has a small thin layer of grease on it also.
My creaks in the front on my ST400 always come from a loose headset but mine is a sealed cartridge unit....