Knee Pain Muscle Imbalances

First of Ive got very flat feet and a leg discrepancy left leg is about 4 mm shorter (also get shin splints from just walking) Ive got orthotic insoles with a raise on them this has sorted out allot of the problems with my ankles and legs.

I have pain in both knees moslty in my left.the left leg has pain under the knee cap and around the left side,the right is just under the knee cap now and then.

With the left knee it hurts when am sitting down properly both feet on the floor and sometimes when I squat if my form is a tiny bit of ,sometimes I think its not the form it’s just my knee
the right leg is just every now and then.

Now it doesnt hurt that bad its more annoying ,it feels like theres pressure on the knee cap if that makes sense.

Now Ive been the docs and they sent me for an xray nothing come back and then Ive been to phisyo 2 diffrent times for few months both times.
The 2nd time I went to phisyo they told me I had muscle imbalances and give me these exercises to do.

ex 1
lie on the floor or bed and push knees downwards hold 30 sec x 5

ex 2
hip raise

Then advanced onto one legged raises.

ex 3
lie on your side leg on top of each other slight bend in your legs and raise the top leg up and down

First time I went I got givin a band to do leg curls with and got told to hold my fist in between my knee and squeez.

Tried it all and nothing has worked.

So any one got any suggestions ?

Nobody can diagnose or treat you online. I’m in the process of going through something like this with my knees; it was going to an orthopedist that got me a dianosis which has led to me actually starting to get better.

I know that but maybe someone has the same type of problem as me ?
Am thinking it mite be chondromalacia.But Ive done the exercise(what I know off) for months and nothing worked then tried them again with a few others a year later.
When I go the doc they just say do you want to go back to phisyo,but phisyo doesnt work.

Do you think just ask my doc if he can send me to a orthopedic?

Also do you know of any exercises to do what work the ligaments/tendons around the knees ?