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?
The easiest way is just use a recipe for lemon cookies. I'm sure you can find lots of them online. If you really want to use a recipe for normal cookies (because you really like it), you could certainly add lemon extract to a regular batch. Don't add too much, the flavour is really concentrated. Since you won't use a lot of it (a teaspoon will do), the liquid:dry proportion practically won't change, but to be sure, you can cut back the milk by the amount (e.g. a teaspoon). You can also add a bit of zest without a problem.
I wouldn't add lemon juice because you're adding milk in your cookies. The milk would curdle (in some cookies that is exactly what you would want to achieve). However, you can try to add lemon juice instead of milk.
Since lemon is acidic, you would want to reduce the quantity of baking powder and add some or more baking soda to neutralize the acidity.
What if you add an acidic ingredient to a recipe with baking powder? You will need to add a little soda. Let's say you are making cookies and substituting 1/2 cup lemon juice for the water in order to make lemon cookies. The recipe calls for 2 teaspoons of baking powder, but you will need to neutralize the acid in the lemon juice. Substitute baking soda for one teaspoon of the baking powder. Corriher says that baking soda is 4 times as powerful as baking powder, so use only 1/4 teaspoon baking soda for each teaspoon of baking powder in the original recipe. -- from http://www.thekitchn.com/pantry-basics-whats-the-differ-40514
What I ended up doing was taking my base sugar cookie recipe and substituting soymilk for milk to prevent the curdling issue. I then divided it into four portions, putting one straight into the fridge unmodified. One portion received zest, one received juice, and one received zest plus juice. The juice cookies may have been softer than the zest cookies (but there were some issues with baking that could have caused that), but all cookies rose the same amount (not much at all, by design). Sure enough, the ones with more lemon tasted more lemony :) Thanks for the help, everyone!