The VMO (vastus medialis) theory was long ago debunked. You cannot selectively train the medial portion of your quad, nor does it selectively atrophy. There are many neurophysiological reasons for this, but I won't go into that unless you would like me to. The primary culprit of poor patellar tracking actually comes from weak HIP muscles: the patella is embedded in the belly of the quad and does not really go anywhere. The issue is that with poor performance of the abductors and external rotators of the hip, your femur actually internally rotates UNDER the patella and causes a relative lateral tracking of the patella and the condyles of the femur. This is a major cause of ITB syndrome, overpronation of the foot, "hip bursitis," and patellofemoral pain syndrome.
I started a blog that I never learned how to work, but there is actually a single PT post there that has some of this info, good pictures, and a demo of nice hip strengthening exercises (by the way, if anyone wants to help me figure out how to make a blog work, ill provide free PT care!)
Now, on to your boot question...
It turns out that taller, stiffer boots actually transfer a great deal of unwanted forces to both the hip and the knee. Under normal conditions the very mobile foot and ankle compensate for uneven surfaces, as well as flexing your leg over your foot during walking (called dorsiflexion). If you wear higher boots you limit your ability to dorsiflex, thus tranferring all that force through the knee and the hip. So...in a "normal" condition, the higher boot actually causes more trouble than it helps. If, however (there are tons of ifs in orthopedics), you do have some underlying condition anywhere along the kinetic chain (back, hip, knee, ankle, foot) then you may need something different. But no one can tell you that through a forum.
But first, I'd give the hip strengthening exercises a try. Most hikers should do these anyway, as most of us are weak here and this is a major component of so, so many lower extremity and back pain problems.