Sounds like a good start!

With the shoes, you could get clips, where your shoes clip onto the pedals. Then when you are know that your feet are positioned correctly(yes, ball) but can also have rotation, if needed so your knees track straight as they go up and down. It also makes it a little easier to keep your foot on the pedals, and allow you to pull up as well as push down. In general, cycling shoes are stiffer too. Part of a bike fit is making sure your feet are moving correctly, as well as seat positioning, handlebar reach, etc.

My thought on the PT thing... if you are going to see one again, find one who does sports medicine, the more experience with cyclists the better, and explain you are a beginning cyclist having pain, and then explain your history. I think that might be better than looking for one that treats a lot of hips but not athletes. The goal is to evaluate how you function vs what a cyclist needs-- if there are correctible issues causing that pain. I have knee tracking problems, and its important to keep my VMO muscle strong. I have weak glutes and tight hamstrings. I have left-right imbalances, etc. Each of those can be improved even if the initial cause is unique.