I thought I'd posted but when it didn't show up I re-wrote it, apologies for that.

Can't quit see that the calf strain is directly related to the popliteal issue, but the area behind the knee is a complex area. Not only do the soleus, plantaris and popliteus cross there, but its the end point for biceps femoris. Keep working with your PT and/or massage person.

When you say "pain at 5 and 7c'clock" are you speaking as if I am standing on your driveside? That would mean pain most intense on the downstroke. just making sure I understand.

not having seen your fit it's hard to say, but in conjunction with the seat height check, ask your fitter about reducing the amount of flexion or "ankling" during your pedal stroke. This will keep the gastroc/soleus from activating as much.

just to make sure that the swelling you describe is moderate, and not possibly a Bakers' cyst?