Increasing pain as they day goes on, as you use the leg, whereas less pain in the morning is typical of musculoskeletal pain. This is due to the mechanical forces exerted on your leg throughout the day of moving around slowly stirs up the problem whereas after prolonged rest (eg a good nights sleep) the tissue calms down. this is all normal after an injury. over time the pain should get less intense and should take more physical stress on the leg to stir it up.
Nothing comes to mind as to what might be causing the clicking. A number of structures around and below the knee can cause clicking sensations. I think this would be too hard to diagnose this over the internet and would require someone to really examine your leg.
I would go an see a specialist musculoskeletal physio and get them to have a good look at your leg. Just because it has been diagnosed as soft tissue injury doesn't mean you can't get relief and improved function from physio.
All the best with your recovery