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.

Scott

A few additional thoughts on this- (I’m a PT in Seattle who specializes in treating runners/endurance athletes and working with gait/movement issues)- I agree with Scott that changing your running speed can dramatically shift your running technique, and slowing down takes some time to get used to. It takes some effort to learn how to run slowly well but definitely can be achieved- I experienced this while training for a 50 mile ultra. It’s hard to say over the internet without seeing you in person, but a common problem I see with runners who have ankle and knee pain during slower paces is lack of a.) calf strength (can you do 25 single leg calf raises consecutively and without form loss?) and b.) decreased Achilles tendon elasticity. Not decreased range of motion- but decreased “bounce” if that makes sense. Hip and core strength are also key, and an often overlooked but crucial factor is often torso and hip posture as well- all of these things can affect the forces going through your knees and ankles and overload those tissues. I like the suggestion of training by hiking uphill instead of trying to run on flat ground – and alternating run/walk technique.