So you have salt & pepper in the recipe but don't say when to add. Whenever?

I think the salt and pepper would be added to the butter mixture along with the flour, which forms a roux for thickening the chowder. However, I don't imagine it is the exact timing is that critical - they are seasonings which can be decreased or increased according to your taste. If the roasted chicken is from a store, it likely has a lot of seasoning already, and some brands of stock are salty. That being the case, you would want to reduce the amount of salt you add. You are using unsalted butter, which will give you some more control over the matter since you can't always predict the seasoning of purchased pre-made ingredients.