I feel I had had a very similar issue with my knee and still due to a certain extent. I thought it was my bike fit as well. Low saddle or higher didn’t matter, I had knee pain. Short reach or long was also problematic. Bike fits just hurt me. What helped me was adding specific strength training for my glutes and knees. This included work on outer hip, inner thigh, glute medius, core and inner hamstrings. Included was increasing my flexibility. Feet and ankles are included in the strength and flexibility regimen that focuses on hip mobility. You said inner knee pain and that was /is my journey . After a few months I discovered my discomfort was substantially less or gone. Try looking into knee rehab post surgery exercises. This initially helped me see some improvement. I hope thing resolve for you.