Very impressive, as is your dedication to getting it right. What was wrong with results from stitching software, like PTGui?
The first thing is that it was impossible to get pleasing colors in both shadows and lit parts with a single raw conversion per frame (except for the foreground where I decided to keep bluish shadows that are more natural). So I had to overlay frames anyway to handle that part.
The second thing is that C1, that I initially intended to use for all conversions, was unable to handle purple fringing in the strongly backlit trees, raw Developper did a much better job on that part. So more overlay to do there.
Finally, I had to use two sets of images to handle the DR of the scene (I had shot 3 images 1 stop apart from each other, but ended up only using the darkest and lightest ones). I tried both the Fusion and true HDR rendering of PTgui, as well as the Autopano Pro auto HDR, but I couldn't get something pleasing with either.
In the end, hand overlay was a much better option that would have been reasonnably fast had I decided to go that route since the beginning. I guess that this is the good thing about being mostly an amateur, I can afford to waste time like this to get an image the I want it to be.