In response to your specific questions:
- Depends on the densitometer. Obviously for B&W materials white light is common. You should do OK with a green of around 550 nm or so.
- Contact or photograph a step tablet. Contacting limits your calibration to just the film, photographing adds system flare.
Scanner optics may cause error due to callier effects. Graphic arts densitometers use diffuse measurements, a plate reader uses a colimated light beam.
It would be nice if you can define the well locations to the reader so they line up with the patches in the step tablet. I'm sure there is a way to do it even if it isn't documented. Clinical analyzers are usually jam-packed with special diagnostic capabilities for machine testing and calibration, but access to this software is almost always blocked to the common end user.
The reader may not have a density range that is useful for film testing. Although the analyzer may be specified for 3.0 OD, this may be a chemical specification for a 1cm path length and the physical path (liquid depth) may be significantly less. If you have a 7mm path then the maximum physical OD is 2.1 OD.