well if you're writing them out that is awesome. as for 'knowing' the 14 position system, yes i can play any of those positions and its helped to unlock the fretboard me. i'm seeing notes i wasn't seeing before, seeing the shapes made up the neck which has given me a virtual fretboard map (the 14 position system is quite a an extensive map too).
how long did it take? i think after about 3-4 months i had memorized it all but i have a hell of alot more time on my hands. i wouldn't worry so much about how much time it will take, just set some realistic goals for yourself as you did above and work from there. just remember, actually memorizing the scales and being able to make music with them are two very separate things, both must be drilled.
for improv its great, i'm hardly a master but once you have the positions memorized you should start hitting up the backing tracks pebber has provided on the website and play your scales along with them. pebber has made some great videos directly on that topic which you should look at once you've memorized those scales. you need to practice with those backing tracks as hard as you would practice anything on guitar, it will not only help to ingrain the scales but also give you new musical ideas and it will also improve your ear, which in the end is what we all want to do.
do you have a guitar teacher? it would be great if you had someone to monitor your technique while you practice pebber's scale system.