Hi cadynz, thanks for your reply.
I wasn't involved in any harsh tackles. Since I made this thread I have seen a doctor regarding my knee, and he confirmed what my physiotherapist had said, it was over use. Whilst I was accustomed to jogging long distances, playing football with all the twists and turns and the ball tricks I was doing meant I should have given my legs a rest. I sat down with my legs out flat and tensed my quads, he noticed there was considerably more muscle just above my right knee (just left of the centre towards the inside) than on my left leg, this is something I had never noticed. He said some muscle wasting had occurred.
This alleviated my fears of not only never being able to run distance again but having a constantly weak left leg as well.
I was instructed to continue with the two legged squats, one legged squats and hops my physio had told me to do and to this time not over do it with the cycling, so 30 mins max on a level surface with a gear of very low resistance.
Whilst a world cup debut would have been nice, I'm now willing to settle for a champions league final debut hopefully next season.