pain in the ball of your foot, what shoes are you using, it may be that the shoe is flexing, and you are “feeling” the pedal through the sole, a stiffer shoe or a bigger pedal may help to spread the load reducing the pressure point.
Knee pain is harder to define, it might be use, riding a road bike forces you to pedal constantly so if you build up to quickly the knee hasn’t had a chance to adapt. It might be set up, any small error will show up because you are pedalling constantly.
Layback shouldn’t be an issue in itself, KOPS is only a guide and not a law.