I just joined and saw your problem.
I had the same problem. What makes it worse is if you have thermal compound on the processor plates and it doesn't make contact with the heat sink, the compound will act as a worse insulator than air alone. It seems that there is a lot of variation in this area from machine to machine.
I found the problem to be that the recessed (or you could say stepped) area of the two "ears" with the screw holes on each side of the heat sinks are too thick to allow the flat part of the heat sink to dip down far enough below the plane of the backplate to contact the processor plate. (Hope I described that adequately.)
I used a flat file to remove some metal from the recessed area to solve this problem. It is very labor intensive, as you have to file the ears, apply the compound to the processors, attach and tighten the heat sinks as if you were finished, then remove them and inspect the spread pattern of the compound. You have to keep filing, installing, uninstalling, and inspecting until you achieve near 100% contact. You might have to file one side more than the other based on what you see.
Tips:
1) Remove the 3 screws from the fan motor and take it off of the fan assembly to keep the assembly from wobbling as you file.
2) Avoid taking too much off at one time. If the ears get too thin, the backplate will be loose when you tighten the heatsink screws.
3) Do all of the filing away from the unit. Carefully remove all of the metal filings between each filing session using a brush or air pressure to avoid getting any filings on the mother board.
4) To conserve thermal compound during all of the fit testing, next time I would use something cheaper to do the testing like automotive bearing grease or Crisco. Just be sure to clean ALL of it off before applying the real thermal compound when you're done.
Good luck!