@ 2contagious
They replaced just the heat sink, which had the fan built-in. There was no need to replace the CPU/RAM tray. I confirmed that they would also check the thermal paste and the verified that they would.
My advice would be to document your concerns on paper. Be prepared to offer a structured and compelling argument. Take detailed pictures of the fan or fans that you are concerned with or are in question.
I am not sure how far the local Apple Store is from where you live, but here is what I would recommend. Complete the check list I mentioned in paragraph 2. When the check list and inspection from your side is complete print everything out, including pictures, and go to the Apple Store. Ask to speak directly to the manager. Tell him you have some concerns with your Mac Pro and use the evidence you gathered from paragraph 2. In addition tell him you did not think it was necessary to drag the Mac Pro all the way down to have the Genius team check it out and that you were 100% certain that these were the parts that need replacing. Tell him that you would do it yourself, but Apple handcuffs you from access to their spare part system and you are forced to work directly with Apple. You can back that claim up by telling him you use your machine to make money and cannot be without it for more than a day; and wether it is true or not is up to you, but it was in my case. Be cool and control the flow of the conversation, just state the facts from your side and then let him respond. More likely than not, he will oblige. If he does not, be prepared to remind him you just spent over $4000 on a Mac Pro.
Now that you have negotiated a repair based on your terms be prepared to hand your Mac Pro over to the Apple Store. I am neurotic about my Mac Pro, and I am sure you are to. Therefore, when you hand it over to the technician, kindly tell him, and you can even do it jokingly, that this machine is your baby and that you would appreciate that they handle it with care. The cool thing is they will laugh but take you serious. In addition, before you hand the machine over, ask them to verify the parts they ordered by bringing them out and then remove the side panel and make an agreement that you are on the same page about what parts are being exchanged.
If you have any other questions let me know and I hope that helps.
Edit: Sorry I missed the part that you were going in on Wednesday. Is that next week Wednesday? If so, you stil have time to complete paragraph 2. Apple Store are able to get spare parts from their distribution center usually within 24-48 hours. So worse case, now that it is the weekend, the parts get ordered Monday for delivery by Wednesday. And now that I am typing this I see you are in the U.K., okay then... I would still use the same approach. The customer service environment from Apple is a corporate thing that they drill down from Cupertino, so I would feel confident that whatever you experience in the US, you will experience in the UK, Asia, etc.
