Welcome back to the bike. I had a TKR 15 years ago at 60 and began riding 12 years ago later going to Speedplays. Never had a problem so perhaps not much help.

Not sure why you have the pain. As you likely know there’s a period of adjustment for the whole body. If you started slowly and built up muscles perhaps it would work. There are too many variable to nail the source of the problem. Could be the TKR, how you ride or something else. Being able to ride without pain is good so perhaps flat pedals is the answer.

Haven’t had rotator cuff problem however shoulders need strong core. Have you worked on your core? Also have y0u had a bike fitting? If not strongly suggest getting one with latest tools. Oh the fitting could help with the pedals. Are yuur legs the same size? If there is a difference that could be the source of pain.

Wish you luck After the fitting (or if you’ve done one) have an expert observe you riding might identify corrective actions — assuming you’ve been riding for a few months to give your body time to adjust to the ride.