Changing gait or stride dramatically, especially if you are forcing a run stride when you could walk at the same speed can very easily lead to the kinds of issues you’re referring to. I assume you’re running slower because you are trying improve your basic aerobic capacity. While this can be done running it can also be done hiking and even fast walking on the flats depending on your aerobic state.
Knee pain is often related to the hip stabilizer muscles; Tensor Faciae Latae, Glutius medius and glutius minimus. All of which act to control the internal and external rotation of the femur in the hip joint. It is possible that the gait changes you have made are causing tightness in these muscles to manifest in knee and ankle pain. I’d start with an aggressive rolling routine on the lateral hip and later quads. You can use a foam roller or a lacrosse ball. My go to rolling tool is this https://www.roguefitness.com/mobilitywod-super-nova-80mm.
If you find the rolling excruciatingly painful you have probably found your problem and only more rolling will eventually loosen things up and get you back to running. It may take a several session to begin to feel relief but the more it hurts the more you need this sort of maintenance work.
While getting through this injury I suggest adopting a run/walk program where you alternate running and fast walking for these aerobic base runs. Try running for 2 to 3 minutes then walking for 1 to 2 minutes. As the injury abates you can increase run time.