First I lower analog gain registers severly causing it to act as 10bit?(maybe lower). What happens is highlights will take a hit and get clipped. However this move will clean shadows by a lot. I matched each file by modifying also cmos 0.
Lowering analog gain registers will improve the DR... until the clipping point starts to drop. This is the sweet spot for ADTG gains. Without any other tweaks, when starting from ISO 100 in photo mode on my 5D3, this method improves the DR by about 0.37 EV, reducing the ISO to 77 (i.e. you should scale the original ADTG gains by 77%). On other cameras (possibly other 5D3's too), the numbers will be different.
Further reducing the ADTG gain is not going to improve DR any more; it will start to decrease the clipping point instead (and that happens in way that tricks the white level autodetection routine from raw_diag, so take the measurements with a grain of salt). Once white level starts to drop, DR is going to remain roughly constant, then it will start to get lower and lower (causes: analog noise and quantization error).
Now, if you set the ADTG gains to some very low value, but you keep the old (i.e. close to 15000) white level, this will result in a dark DNG. You might think you've just got a lower ISO, so you may be tempted to increase the exposure time and compare the shadows. Yes, this increase in exposure time will give *much* cleaner shadows. Once you look at the highlights, you will realize it's a false alarm.
When comparing noise at different flavors of ISO 100 (or any other ISO), make sure you capture the
same amount of light (i.e. same shutter speed, aperture and test scene). This is important, otherwise the difference in noise will be given by the different amounts of captured light (i.e. the test results will be... well... bogus).
Then, render the two images at the same brightness on the screen, but you already did that.
