Thanks again for the great feedback, thisisatest.
I moved my cleats back in so my shoes are now further from the bike. I took a video of my lower back marked with a piece of tape, and it stayed pretty static, so I guess I'm not hip rocking too much. I lowered my seat back down 0.5cm, just to be safe. Now I'm at 1cm higher.
I tried riding on Thursday after the 1.5cm rise, and again today after the 0.5cm drop. The anterior knee has become worse
than ever during both periods. I'm not to sure what the problem is now. Now that I have straightened out my pedal stroke, I think I'm either putting more pressure on my anterior knee, or my knees are not used to moving straight and I'm straining some unworked tendon in my knees. I'm really confused, and the knee pain has now become unbearable.
When I orginally got fitted my fitter had me at 73cm which had my extension at 35 degrees on the down stroke, he told me to raise it another 1cm after I got a zero setback saddle, and now I've raised it another 0.5 cm from there (so 74.5cm). I thinking I'm probably somewhere at 15-20 degrees now. I've never heard of any someone getting anterior pain from having a saddle too high, but maybe I'm wrong...
I don't really have time to make a trip to my fitter until May, guess I will have to take a break from riding if I can't find any sort of solution until then.