What is the best way to add lemon flavor to a cookie recipe? I know lemon juice is highly acidic, I don't want to throw off the PH of the dough. Is lemon extract the same way? Lemon zest? Is there a way to compensate for that? 
Try using lemon zest (lemon peel shavings) and lemon or lime juice.  You might try sprinkling the zest over the top of the cookies right before you put them in if you don't get enough flavor from adding it to the batter 