Intense popliteal pain

Alright I have been suffering from popliteal pain ever since I started doing close to 50k rides. Now getting on the bike for 15 minutes causes pain. Been getting treatment for a few weeks now but it's not getting better. Straightening my leg hurts after riding for a few days even. Getting on the bike once and it's back intensely. I have had a specialized bg fit done but had it done before I even began cycling. What can I do? My right knee is the biggest culprit when on the downstroke my knees turn inwards its part of my anatomy since i had a broken ankle when younger my left knee not as severe of a rotation but still developing discomfort I have a bmc bike with speedplay pedals I've opened up the float and moved my cleats further back thinking I'm over loading the calf. The movement is better foot stays flatter on the downstroke as opposed to toes down. Should I lower my saddle until my knees don't rotate inwards and slide my seat further back? I'm going on vacation for three weeks so I hope that gives me time to heal but I do want to get this resolved or else I might have to give up cycling and sell all my stuff which I just bought.

 

You need a better bike fit. You may need shims on your cleats or wedges in your shoes to get your knees to track properly. Many things can cause knee pain. A good rule of thumb front of knee, seat is to far forward or to low. back of the knee, just the opposite.
Talk to your original fitter. If things are that bad he may look at you again for nothing. I doesnt help his buisness if you stop riding due to a poor fit.
gl.