Less than 7 weeks to IMFL and NOW starting to have knee pain on bike

I have been experiencing some strange knee pain on my long bike rides for the last 3-4 weeks now. It started during one of the long rides, probably about 80 or so miles into it (I've done 80's before - it was not the first). I've had issues witch chafing on the bike and was shifting around more than usual on the ride. In hindsight I actually think that the shifting around and pushing the right knee out while being clipped in did something to my knee. The pain is in my right knee only and is mainly there when I push down. It goes from being there sometimes to being excruciating if I want to stand up and push down for climbing. I've since been back to my bike fitter (even though nothing has changed on the bike setup) and explained the issue. He said that this sounds like something that is being caused by leg discrepancy (which I know I have but we have never done anything about it since it's not much and it was never an issue), but he is also baffled why it would affect me now. I do sit slightly more to the right, so he put a little shim under my right cleat to see if this would solve the issue.
I went out for a 80 mile ride last Saturday and about 60 miles into it the pain started again. It's just on the outside of my right knee, goes slightly around the back of the knee/upper calf and the sometimes radiates all the way to my ankle. At times it feels like I am trying to ride with a broken leg.
The good thing is, that it does not affect my run at all. I can get off the bike, hurting, and start running just fine.
I am doing Augusta half in less than 2 weeks and I am doing FL as my first full. I am so stressed out about this now. What do I do? Keep biking (could I make it worse?), or take a break (I don't really want to as now comes the real meat of the bike rides), see a doc? (Orthopedic?)