The most likely part number is 661-4687, which can be had new for about $1100.
You can get the board repaired with a 6 Months warranty on parts and labor for $595 + $40 shipping
You will need the original software installation disk for the fans syncing software to do it yourself. I'm using the same machine right now. I would think a reasonable labor repair rate would be about $300 - $350. + shipping and packing. At least that what I would charge a customer. Wood blocks are best to prevent the handles from getting crushed and insure it! I don't think anyone has done a guide on this machine as logic board failures are rare and so is the machine.
All your hard drive data should be fine. Please tell us why you think the logic board has gone bad. What tests did Apple do? Did you actually see them do it. Was it an actual Apple store or an Authorized Service Provider?