(1) Are the R-07 preamps as good as the Zoom F3's? Your idea is all about optimising gain staging with the R-07, but your results will still be worse if the F3 provides cleaner gain. You could use a cleaner external pre-amp like most of us have done in the past, but then you add to bulk.
Obviously the F3 preamps are substantially better. And no matter what processing you do after the ADC's: It will not improve the preamps. However, what I think the software program would do is 'helping getting the best out of your R07'. Until now the 'safety track' has been considered merely as a backup in case you set the levels too high (probably helped by the name that was put on this track by the Roland marketing department). My idea is to consider it as 'just a 2nd ADC' like is implemented on the 32bit recorders like the F3. Let the main track clip and unlock/profit from the extra 20dB headroom that's in your R07! It allows you to set the level higher and therefor beat the noise (I hope)!
(2) How much work would it take to write a piece of software that accomplished what you're proposing automatically? Because doing it all manually would be a huge pain - not worth it at all unless you absolutely had to. If you are willing to actually write the software, though, it's a good idea!
It doesn't seem like rocket science and the heavy work of reading/writing audio files can be outsourced to available libraries like libsndfile. It depends a bit on how fancy and fool-proof it has to be, and if it should run on Linux/Windows/Mac, command line or graphical user interface etc, but I think a couple of hours work would be enough to get a working prototype... It would be fun to make, I just started a bit already.
The availability of real world example input files would be very helpful for testing! The recording described by Roffels seems like the perfect example: High dynamics and a clipping main track.
@Roffels: Do you still happen to have the main and safety track of the recording you described? And if so, would you be willing to share these with me for testing? That would be awesome!