With the moral quandary ultimately in your hands alone, what happens from this point is certainly going to be what you decide to make happen, but since you are asking... when the money is covered - certainly at your end and possibly at his - then the only point of ethical uncertainly for your consideration is keeping the parts that you have now both received and been compensated for the loss of, which would be problems whether they were perfect or junk... I think I would be inclined to ship them back - if, as Steve says, they conformed to the description I had bought them with, probably with a note pointing out anything I thought rendered the parts unusable (so that the vendor might feel obligated to amend the ad if it seemed misleading or unclear). I realize this puts you out of pocket on the shipping - but if shipping was $3 instead of $40, i imagine it wouldn't be an issue, and if the shipping costs themselves are what is at the center of the dilemma - then that is NOT a moral question, but rather an economic one; a different matter entirely. (The argument that what freight costs are running is highly immoral aside, for our purposes)
Moral questions are interesting - I think about those all the time; I was even considering the recent installation of a trailer hitch on my old Dodge as a matter of right or wrong in the eyes of a just society... turns out it's ok, ethically, but it shouldn't show too much.