egg beaters and pearl izumi's.

my other bike is 52 X 18

Weight training actually helps strengthen the knees quite a bit, as your leg muscles get stronger they take more weight and strain off your knees.

With no significant change in gearing, and the same shoes and pedals, I would then look into whether your cranks are bent (or possibly a different BB spindle length causing a shift in knee/pedal alignment).

And I know it has been mentioned, but relative saddle position should be adjusted to be similar to your old bike's setup and then tweaked from there.