With regards to HDR, although my camera has a 3 shot bracket facility, I prefer to do it manually. What I do is set my camera to AV (Aperture, not sure what it is on Nikon) and take readings for the brightest and darkest areas. I then switch to manual and take photos at 1 stop intervals between these 2 points. I then use Photomatix to merge them, don't worry about slight differences in position as the software will line it up. If your tripod has a hook on it, you could always hang your bag off it for stability. Also use a remote release or timer to take the picture, (mine was about £8 from ebay).
Its good that you use RAW as it gives you more flexibility to recover shadows and blown highlighs. Can't comment on aperture as I'm not lucky enough to have a mac