Hate to hear you had to learn this lesson on a clutch but this is why service shops mark up their parts. If you had brought the car into the dealer and had them replace the clutch and supply the parts to do it, yes you would have paid more for the parts. But when it died 5K later, you would have got a free replacement and the dealer would have had to eat the labor cost. Trust me the Ford dealer can scream at Ford Parts all they want for losing labor dollars on a early fail on a Ford part, but Ford will not reimburse them for the lost labor even when Ford supplied a defective part. It's a cruel world out there.
I fix computers for a living and I have to explain this to people at least a 3-4 times a month - and I'm selling exclusively to businesses who you would think would know better. Yes, I can see that HP sells the same PC as I'm quoting you for less money than I'm quoting. Yes I'm going to charge you for labor a second time if you buy the Dell and supply it to me and I set it up and it dies a week later. You can assume the risk or I can assume the risk, which do you want?
In your case, you benefited from the cheaper price by sourcing the parts yourself. But in order to obtain that benefit you had to assume more risk. In this case the risk the part might fail. There is no free lunch.
In the long run the parts markup by the dealer ends up paying for the labor lost to the comebacks under warranty, so while it may seem like the service shop is gouging and overcharging on the parts cost, they don't get to keep it, trust me. :-)