I have started some research as the result of correspondence with another member of the community and we came to realize a few things about the Autopy toolset.
1. Avoid the Orange/Red loops at all costs as they guarantee spiral edge loops.
2. Try to keep all Green Strokes flowing in the same direction for major sections
3. Splitting your model up into pieces can improve the topology results.
Later I was working with these concepts (forgot about the splitting model up one till now) and I came across another interesting thing.
Autopy likes to follow density painted areas.
This started me on some testing and below is a video with the results that are actually pretty good considering. Hope that you all enjoy and are able to help tweak this system even more.
p.s. vid is still uploading if it isn't showing up yet .. it goes for 24 minutes sorry for not clipping down the work.. I personally like to see things from start to end though I know some people prefer to see the start of a few bits of work.. then timelapse and it's all done.