Once you get 'into it' you might benefit from a Specialized Body Geometry check on your feet.
Expensive, but you can customise the shoe inserts to suit, but you seem to be getting sorted now.
As others have said, your knees are the most important part to get right, and you MUST look after them as a cyclist, especially if you want to do it for a lifetime.
You'll get your setup sorted soon, just remember, a little at a time (miles and adjustments).....
Once 'dialled in' you'll soon notice if a cleat isn't set up quite right...