Interesting explanation about your hamstring tightness and ankle flexibility. That could explain why the toe down style feels good for you.
The tendency to knee pain worries me. Is your job hard on your knees?. Is there anything you can do about it - pads, position?Was that knee injured once?
For more information about knee pain caused by cycling, see here
KNEE PAIN » Bike Fit » Steve Hogg's Bike Fitting Website
Note point 5.