Some little background reading for you. I have had pain in my knees when I upped my training.
http://www.bikeradar.com/fitness/article/take-care-of-your-knees-17010/
http://www.bikeradar.com/fitness/article/take-care-of-your-knees-part-2-17445/
Best go and see a physio and take things from there. It is ITBS that was affecting me with tight hip flexors and quads, but the pain was experienced in my knees. I started a stretch and strengthening programme, and use a foam roller regularly.
See what the physio advises. Take some time off the bike, changing your training programme and perhaps then looking at your bike set-up, maybe even a bike fit could help.
I am not a physio, but lunges and squats are just going to load up and tighten the very muscles you are stretching and loosening with your yoga type stuff. If it hurts, stop doing it and work on something else.