Sorry to hear you're having a tough time, your new problem sounds horrible. I think you may have developed a neuroma or some other kind of nerve pain, from the description of your pain. If you press on the sore spot on your knee does that reproduce the shooting pain down your leg? If it does it's a good indicator that you may have developed a neuroma.
I believe there are several options for treatment of this, usually starting with a local anaesthetic injection into the site as a way of checking that it is that nerve which is causing the pain. If it is diagnosed as that you could have the neuroma surgically removed, or have some sort of treatment designed to kill/numb the nerve. I would suggest asking for a referral to a specialist pain management service and hopefully they'll be able to sort it for you.
Hope you get it sorted soon!