[jfrancho]

1. use your A method in manual mode. One other way is to use exposure comensation in Av mode. Also, you can use auto bracketing in Av mode. Since you are using a tripod and either remote shutter or delay shutter, there is no reason not to be in the lowest ISO available.

2. Spot or Partial Meter the brightest and darkest areas of the scene, noting the shutter speed in each. Those will be your bookend exposures. Fill the gap with exposures one to two stops apart. Make sure your intervals are consistent. Alternatively, you can auto bracketing. I use -2, 0, +2 for my AEB settings. If you can do more with your camera, go for the max.

3&4. Photomatix or Dynamic Photo HDR are two excellent tools. Its worth noting that I generally shoot raw and my work flow is Photoshop ACR to make a 16 bit tiff > Photomatix to make a 32 bit HDR and then tone map to a 16 bit tiff > back to Photoshop for final processing, which can include NR, sharpening, B&D, cloning, color adjustments, contrast, etc.