Thanks for the info. I have been advised to check out someone certified in PRI by numerous people on forum. Right now I am seeing a new physiotherapist who is an olympic athlete and member of the Canadian Physiotherapy Association and is STOTT PILATES Certified Rehab Instructor.  In addition, she is trained in the Integrated Systems Model of Physiotherapy assessment and treatment. She specializes in integrating Clinical Pilates stabilization principles and exercises to rehabilitation. Hopefully she will get me on the right track.

Also just came by this exercise which looks pretty insane,and looks a lot like what I imagine clinical pilates to be:

Update:
So there has been very little progress in the last 1-2 months. I feel like my progress has stagnated and my symptoms arent improving noticeably. I still get a return of symptoms (tight IT band, and painfully achy knees right around the patellafemoral joint) when I load the knee, and avoid doing mobility/foam rolling/stretching/myofascial release. I still cant do any physical activity without intense flare of symptoms. I just recently seen my physiotherapist, and he says we are going to need to take a new approach. He looked at my hamstring tightness while keeping a lumbar curvature (not letting my lower back round). Apparently he found that my hamstrings are completely restricted. In order to get full range of motion for my hamstrings I move my lumber spine to much. He then tried getting me to stretch my hamstrings while preventing my lumbar spine from rounding. This was very difficult to do and co-ordinate. He then had me lay supine with my feet flat on the table and knees up with a blood pressure cuff on my lumbar spine. He had me raise one of my legs while telling me to not move my lumbar spine as indicated by the pressure changes in the pressure gauge. I found it nearly impossible to not move my lumbar spine while lifting my leg. He said that my lumbar spine and deep core muscles are unstable and move around to much leading to lots of pelvic and hip motion, which leads to excessive motion of my femur during dynamic tasks, leading to my patellofemoral symptoms. He then tried to teach my to activate my transversus abdominis, diaphraghm, and pelvic floor by just doing breathing exercises. He noticed I was breathing through my chest and not through my diaphragm. He said my deep core muscles arent being activated thus leading to lumbo-pelvic instability. He said I have poor motor control and I have to learn how to activate my deep core muscles to prevent excessive motion of my lumbo-pelvic complex. 

Glute strengthening
He said continue doing the glute strengthening exercises. I do feel the glutes working when doing the single leg squat/lunge against wall, x-band/lateral side walks, one leg standing fire-hydrants, and clamshells.

Self-myofascial release
Still seem to have tightness in IT band, hamstrings, quads, etc.. Smashing/rolling on lacross ball and rumble roller seem to be temporary solutions and only help a little. Also, been doing E-stimed trigger point dry needling everyday for 15 minutes.

Deep core, transverse abdominis, diaphragm, pelvic floor and lumbo-pelvic stability
He gave me a few exercises to work on for this that I am still confused about. The most important he said is just getting the diaphragm to work for breathing. He said breath with your stomach/diaphragm area rather then chest. Also something about decreasing the belt line (space between belt line on pants and stomach). He said as I get better start contracting my pelvic floor muscles slightly during the breathing exercise. The 2nd exercise is lying supine with knees bent and raising one leg without moving the lumbar spine/lower back. 

Hamstring tightness
The 3rd exercises is doing a straight leg deadlift to help lengthen the hamstrings.

Future:
I made an appointment in a few days with an experienced physiotherapist whose also a pilates instructor and an olympic athlete. She should be able to help with my lumbo-pelvic instability issue and deep core muscle strengthening.

jtrue funny enough my physiotherapist brought up the point that I have slightly weaker adductors on the effected side (side with knee pain and glute medius weakness). He says we want to strengthen the adductors but not so much that they are compensating for the glute medius. He says functional exercises will strengthen the adductors effectively while also strengthening the glute medius. 

Heres a routine I came up with for glute strengthening, pelvic stability and patellofemoral pain syndrome from the vast amount of research I have done and from my own physiotherapy experience. 

8 levels:
1 – Posterolateral hip (glute) muscle isolation (non-weightbearing, activation)
2 – double limb support (static, activation)
3 – single limb support (static, activation) 
4 – double limb support (dynamic, strength) 
5 – single limb support (dynamic, strength)
6 – double limb support (ballistic, movement re-education)
7 – single limb support (ballistic, movement re-education)
8 – sports specific

1 – Posterolateral hip (glute) muscle isolation (non-weightbearing, activation)

Exercises
1. Clamshells 
• neutral pelvis
• bi-planar motion
• use resistance band, progress to stronger band and 60 second hold
2. Firehydrant 
• lift leg to side and slightly back
• maintain neutral pelvis
• tri-planar motion
• use resistance band, progress to stronger band and 60 second hold 
3. Sidelying plank/clam shell hybrid 
• perform clamshell while in side plank position
• dont roll hips back
• engages core

Progression criteria: hold each exercises for 60 seconds bi-laterally

Level 2 – double limb support (static, activation)

Exercises
1. Static squat with hip bias
• hold squat position at aprx 80-90 degrees
• knees slightly greater than shoulder width apart
• use resistance band around knees
• externally rotate knees
• lean forward with torso
• keep torso neutral
2. Static sumo squat
• hold sumo squat position at aprx 90-90 degrees
• lean slightly forward
• toes pointing out

Level 3 – single limb support (static, activation) 

Exercises
1. Hip hike
• single leg stance
• raise pelvis on one side
• hold position 
2. Bent over hip hike
• same as above except bend over by hip hinging and leaning forward
3. Standing firehydrant
• similar to above 
4. Wall stance
• one leg stance with side against wall
• leg against wall is lifted at aprx 90 degrees
• push against wall with the stance leg while lifting pelvis (hip hiking)
• hold position

4 – double limb support (dynamic, strength) 

Exercises
1. Squat with hip bias
• lean forward with torso
• weight on heels
• push butt back
• resistance band around knees
• externally rotate knees
• knees slightly greater than shoulder width apart
• dont track knees over toes
• progress towards weights
2. Sumo squat
3. Lunge with hip bias
• similar to a skater squat or king deadlift 
• perform lunge motion
• lean forward
• weight on front leg and heels
• dont track knee over toes
• keep pelvis neutral (by hip hiking the pelvis on the opposite side as the front leg)
• use something to hold unto for better control, progress towards holding unto nothing and weights

5 – single limb support (dynamic, strength)

Exercises
1. Bulgarian split squat with hip bias
2. standing birdogs
3. Single leg deadlifts
4. Standing firehydrants
5. Hip Hike
6. Bent over hip hike
7. Step ups
8. Step downs
9. Single leg squats

My symptoms are improving slightly, however it seems to be taking way to long. The physio had me do a lunge variation to try to emphasize glute medius activation, however my IT band flared up and knee pain came back really harshly for a few days. It took some smashing/rolling, stretching, E-stimed dry needling, and glute medius activation at home for a couple days to get back to normal. However, after the lunges my glutes were really sore indicating perhaps I was activating the glutes in a way I wasn’t before. But then why the IT band flare and knee pain? Maybe my knees tracking near my toes during the lunge had a role in the flare of symptoms. I have my next physio appointment on Thursday, I will discuss with him in regards to what the lunges did. He is trying to integrate my new glute medius strength that I have gained (from doing isolated and non-functional exercises) into a functional exercises thats why he had me do the modified lunges. I started to do 1 leg stance hip hikes tho as an alternate to the lunges (seems to work the glute medius in a similar way and is somewhat functional). Perhaps the lunges can be the progression after the 1 leg stance hip hikes get easy.

Interesting that you say after smashing your tib anterior your symptoms are better. Seems almost to easy/good to be true that such a problem is fixed so easily with a seemingly unrelated muscle group. I guess I have to give smashing the tib anterior a longer and more consistent try. Perhaps its also playing a role in my symptoms (although I doubt it).

Dan

Nice to hear your well on your way to recovery. Keep up with the glute medius strengthening. Its hard to tell whats exactly the cause of your pain and tightness return. Perhaps cross- country skiing is good for you tight IT bands and lateral knee pain as its one of the few sports that use lots of glutes?