Watch the Summary of Harmonic Minor online guitar lesson by John Stowell from Modern Jazz Improv
One way to connect patterns/ideas/arpeggios up and down the neck is to restrict yourself to bass lines (primarily 1/4 notes) and/or different string sets. Playing a blues using only 1/4 notes on the bottom two/top two, or an inside string set using only melodic minor substitutions can be very instructive.
By limiting your rhythmic and harmonic choices and practicing within a narrrowly conscribed format for 5-10 minutes, some ideas will emerge. Here is another harmonic minor substitution you can try: over a minor chord, in addition to playing harmonic minor of the key that you're in and a whole tone below a minor, play the harmonic minor a 5th above for a Dorian b5 sound. (i.e., over C minor, use C, Bb and G harmonic minor).