Are you also a runner? This is more common in runners but not unheard of in cyclists/triathletes. The popliteus is part of the knee flexion muscle group and in my experience the 'last' muscle to be injured due to over extension of the joint. However, some of its function is to stabilise the knee in lateral movement. In this case for a cyclist some of the therapy starts in the shoe and pedal interface. Moving the cleats back can be a first step, but having a fitter check varus/valgus and cleat 'toe in/out' is important too.

For now, try lowering your saddle 2-3mm (and adjust saddle back 2mm to compensate). Try a short ride in small chainring first.

Curious to know how you injured your calf and which muscle of the calf it was?
Also is the popliteus pain is higher up towards the center of the knee joint or further down towards the side of the tibia? Does it hurt more when pulling up on the cycling stroke?

Your PT can suggest some strengthening exercises with leg bands too.
Anne