Start with the scales. Memorize the fingerings. The Scale tab features A Major Scales all over the fretboard. Don't try to learn it all in a day. You mainly just need to focus on the High Octave Scale(measures 1-4), and the Low Octave Scale(measures 4-8). Use the focus feature in Tunefox to practice those repeatedly.
Leave fingers down as you ascend the scale on one string, and have them ready when descending. In general if a note calls for your Second finger - have two fingers down. It it calls for your third finger, then have three fingers down, etc. The rule will be broken at times, but in general this habit will help you form great coordination, strength and eventually speed. Use only downstrokes with your pick for the Scales. Go for big, beautiful tone. Go slow, the longer you hold fingers down the more the muscle is engaged. This is how you build strength, stamina, and muscle memory. You also hear the note longer which develops your ear.
In the workouts we are using alternate picking. The first examples show pick direction that the rest will follow. Again, the focus feature is your friend. Master the sections individually before trying to tackle it all at once. Do it at a tempo you can handle.