Apple logic board part number replacement issue

Since you've paid for AppleCare - send it in. It doesn't make sense you would be charged for a repair unless there was some sort of external damage, so perhaps you misunderstand the quote.

Perhaps the pricing was for an estimate if the fault was not covered so you could be prepared in case that were the case.

Call back and ask to have your situation cleared up or drop by a store with if one with a Genius Bar is convenient. I would remove the third party RAM and accessories (as Apple will ask you and inspect for before beginning service) before presenting your Mac for service. Inform them you have had a second drive in the optibay and offer to let them have / evaluate the part if desired to ensure it didn't cause the malfunction.

Here are the North American terms of service - and you can see that Apple may charge you a diagnostic fee if you send them a Mac and the failure is due to third party parts being the cause.

I have received my new logic board today and installed it successfully. I also upgraded the Macbook with a 240GB SSD and 4GBs of RAM.

I only encountered 2 problems which can be worked around easily. The first one was the different SuperDrive connector. I simply didn't connect the SuperDrive, but you can easily order the right SuperDrive, since they're not that expensive. The second and most important problem I encountered was the different layout of the heat sink. This needs replacement as well in order to get it working properly. I'm still waiting for this part to be delivered. For now, my Macbook shuts down after a few minutes, because it gets too hot.

After I've received the right heat sink and installed Yosemite, I'll give you guys another update.