The machine I used to document for this thread was parted out a couple of years ago, but it took me a while to get around to writing up the findings. The case eventually went to a case modder who then turned it into a Core i7 thing.
Of course, before anyone starts removing their Logic Board for a BGA repair, make sure you have the correct memory in it first! Incorrect memory or memory in mismatched pairs will cause exactly the same symptoms and is so much easier to resolve.
I haven't attempted to mount a fan on the reverse side of the board before. It's possible something like a small MacBook blower would work and chances are it would fit behind there, but I can't confirm it. Considering the size of the heatsink, a MacBook blower may not even move the required volume of air needed to cool it down significantly anyway.
From what I understand, there is a cut-out in the metal that separates the Logic Board area from the Optical Drives / Hard Drives. The fan in the Optical and Hard Drive area can draw air upwards and over the chipset heatsink fins. I haven't smoke tested the case to verify the airflow or seen any Apple documentation yet to confirm this either, but it's what I've heard.
I think the U3 Memory Controller / Bus Bridge (aka. the Chipset) uses thermal paste. I recall this being the case from when I stripped my machine down at least. It's entirely possible that the Thermal Paste will have dried out by now, so if you can replace it, it's probably not a bad idea.
The challenge is that the chip sits behind that heat pipe and heat sink arrangement, and it's secured to the Logic Board with plastic pins that are rather easy to break if you're not extremely gentle. If they break, you'll have a really hard time securing the heatsink to the Logic Board, which is even worse for thermal transfer than having dried thermal paste. Not to mention extracting the entire Logic Board is a challenge in itself, requiring removal of the processors and a number of other components. So unless you can handle working with delicate electronics, I'd avoid messing around with it for now.
At least it sounds like you've taken care of it, making sure to avoid flexing the board near the memory slots and cleaning the dust out of it from time to time. Hopefully it won't require any major repairs for some time yet.