NDVI Radiometric Calibration and Image Optimisation

Continuing the discussion from Inspire NDVI problems:

This previous topic brought up some interesting challenges for NIR imagery capture using NIR filter lense altered cameras. Also the FAQ for DD debates some challenges with these cameras. http://support.dronedeploy.com/docs/ndvi-cameras. However many people have been using these types of cameras successfully including sensefly UAVs prior to the availability of sensors like the Sequoia which is due in May 2016. So how is it being achieved?

Keen to work on a best practices capture workflow. Many of the blogs and help articles focus on the issues but would like feedback on the best workflow to at least reduce these effects.

Welcome feedback on the following:

Time of day: 10am to 2pm (minimise shadow)
Weather: 100% blue sky, or possibly 100% overcast cloud to ensure illumination remains the same throughout capture.
Camera Setting: ISO: 100 (to reduce noise), Shutter: (1/200 or faster), Manually set white balance: SUNNY or CLOUDY (depending on weather).
Image Format: Ideally RAW images as opposed to JPG as you can process RAW into TIF and correct for White Balance issues etc. and vinaigrette in the lenses. But most “autopilot” mapping apps do not allow for RAW images so this is up for debate on the best practices here and the real benefit in doing this?
Radiometric Calibration: Before flight take a picture at ground level of a calibration target. For example a 18% grey white balance card. Ensure the card takes up the full lenses view, thus being able to later correct for any vinaigrette in the lenses (darkening around the edges using software), and image colour balance. But the trick here is knowing the values of this material should be for a NIR camera vs a RGB.
Conduct the flight: If there is any change in weather conditions (illumination) during flight then you will likely need to refly?

Thanks again, and welcome any debate on the best flight workflow for a NIR filter lenses camera.