poita, thanks for sharing all this info. Its great to read.
Mind if I ask some questions:
What format are you capturing in; Tiff? I assume the full bit depth of the camera, 12-bit?
Why are you triggering the LED light source instead of leaving it always on? Is it to save on the life of the LED?
Concerning audio, I know you can transfer the optical track to PCM/WAV using freeware software but would that software work on optical tracks encoded in Dolby noise reduction?