Dylan, I have some of the same problems due to a femur fracture I sustained back in 2005. Learning to rebuild and correct the faults of my bad leg has made me pretty aware of certain things. The big thing is definitely strengthening your feet and areas upstream and downstream e.g. quadricep(rectus femoris,VMO etc), calf muscles etc. Also, since my foot and ankle and hip areas are still not 100% my calves have to work overtime. When my tibialis posterior becomes tight it is no longer active which leads to overpronation of my foot(collapsed arch)which then leads to my knee bowing in (valgus knee). Also, if you’re missing internal rotation then your running form will suffer because you won’t be creating the right force to press off during your stride. I try to do 5:00 cumulative calf holds every other day to help build up my tibialis posterior (B McKenzie suggests this in a video).
With regards to running form I try to let my heel kiss the ground as kaitlin suggested. Essentially, the quieter you are when you run the better. You’ll notice people with bad running form or poor mobility will be really loud when they run. Yesterday I was running trails (which requires a more upright torso) and felt like I was stomping the whole time. This in turn also led to greater spinal loading which did not amuse my lower back muscles or my TFL. So I definitely have to mobilize areas daIly that I know are going to be responsible for keeping me efficient and injury free.
Sorry if I’m being long-winded but hopefully this helps and I try to watch at least one MWOD video per day to assist me in getting back to Supple Leopard status. If you have any questions or need me to suggest any videos for you to delve into let me know! We owe it to ourselves to be the best biomechanical creatures possible.

Travis