As for as the sequence of learning scales, arpeggios, pentatonics, neck mapping, and improvising I've put together the following plan for my own personal study.
Learn the open position scales first. Use them to learn 25 to 50 fiddle tunes in open position (or 100, 200?). Run through the scales every day and create variations from them until they become completely second nature. Now is the time to really focus on proper right hand technique which IMO is the most important key to becoming a good player.
At the same time start doing the Aonzo scales every day. This will prepare you to advance up the neck and help develop the pinky finger which is a absolutely necessary step to becoming an advanced mandolin player.
Next, learn the arpeggios and be sure to associate them with the chord in each position up the neck. This will help you start to develop a mental picture of the entire neck and how everything is interlocked.
Now it's time to learn all the doublestops for every major chord, again, associate them with the chord shape as you go up the neck.
To tie everything together it's time to learn the pentatonic scales because you'll be ready to associate them with the arpeggios and doublestops you've learned and get you on the improvising trail.
Last, learn the complete "position scales" for the major keys all the way to the 16 fret. At this point you'll have good use of the pinky finger and be able to handle the difficulties of position playing. A good way to drill these scales into your head is to play simple fiddle tunes in each position as you go up the neck, this will help build permanent associations that will be valuable tools when you are improvising.
Now you'll have a good basic knowledge of the fretboard and have the basic tools to learn to improvise over most progressions.
After this it's on to jazz or classical studies...