3 shot (camera JPEGs) stitched with Microsoft ICE. I used a tiny tripod like this
For hand held shots I'd use multiple shots, 10-12 shots at the slowest speed you can held hold without blur will clean up the noise rather well. It works best with shooting RAW and converting the images without luminance NR to preserve sharpness.
You can use the cameras multi-shot noise reduction, but I'm not very happy with it. I use a piece of software called Photo Acute 3 which can align and combine the shots automatically.
No, I pick my focus area. Either with the movable focus box, or with manual focusing and peaking. When I do several shots for stitching I focus on the main target, then switch to manual focus (and lock exposure), so all the shots have the same focus distance.