Hello again, all!
I just ran some basic tests regarding the temperature of the internal components. Keep in mind that is very subjective, since I do not have a thermal probe or any way to effective measure the temperature.
I run half an hour with Gear of War (very GPU demanding) with the console open but with the MoBo in the inner shell. After this period of time I decided to check the sinks. They are very hot, I can not even touch the GPU sink. The memories on the upper side of the motherboard, outside of the sink, were warm. Quite warm, but not hot, I can touch them easily. And after a second on two the memories were simple cold again, they cool down very fast. The GPU sink however, was still very hot and I can still not touch it. I know that this test is as imprecise as it can be, I need to get a proble asap, but this seems to confirm to me that the hottest components are the GPU and the CPU. The memories can get warm, but not really hot, and cool down quick. I was unable to check the memories in the back of the MoBo, but my guess is that they run in a similar temperature.
Back the pads: I am pretty sure that thermal materials would be better for the mod, but the rubber for the sake of testing is fine. I do not believe it will warm that much the memories even after a long period of time (mine is 4 months running that way).
To the ones trying the method: make sure the pads are a little bigger than the memories. The pressure has to be applied at the edge of the memories, specially the ones at the side of the GPU.