Help! I've used self raising flour instead of AP flour for base of lemon bars - should I still cook it or toss it and start again?

As you probably know, self-rising flour will contain baking powder to help your baked goods rise. If I remember correctly, the lemon bar base is supposed to be a bit dense and, as a result, doesn't contain leaveners. But, I wouldn't toss the base unless you want absolute perfection; move forward and see how it turns out. :) (serious bakers may disagree)

And dont add any salt if asked for in recipe since self rising flour has salt.

Dont toss but your lemon bars will be more cakey due to the baking powder in the self rising flour. Should still taste awesome.