Possible conclusion that can be made: The right glute medius isn’t being activated or firing properly thus explains why I have knee pain symptoms on my right knee only. 
Solution: 
1) Learn to activate my right glute medius
2) strengthen the right glute medius, 
3) and then integrate the new found strength into functional activities.

I am focusing on 2 major exercises to address this issue (I am still doing my routine but with a focus on the 2 exercises below):
1) Clam shells (focus on right side)
2) X-band walks
3) Increase hip external range of motion on right side (Capsule stretching doing banded distractions, hip openers)

Since I have been doing the clamshells I have feel my right glute medius being worked so I know I can activate it. I guess its just a matter of keep working those exercises until I can strengthen it a sufficient amount and then finally integrate the new found strength and learn to activate it during functional exercises (squats, single leg squats, lunges, walking, running etc..)

I will keep with the routine and additionally focus more on the above exercises for 1-2 months. After 1-2 months I will get the 3-D gait analyses re-tested to see if their has been improvements made. If their hasn’t been major improvements in both the gait pattern and/or my symptoms I will look into getting a full length foot lift on my shorter leg.