Could somebody help me with some overheating issues – Sony Vaio laptop?

So I’ve got this Sony Vaio VGN-CR26GN_B that I’ve had for about two and a half years. 90% of the time I’ve got it on my desk plugged into a monitor and keyboard etc. and I use it as I would a desktop. During the other 10% of the time when I’ve got it either on a bus or at work or on the couch etc. I’ve noticed that for the last few months the system would just shut down randomly. I did some searching and apparantly when it senses the CPU temperature reaches a certain level, it shuts itself down. That’s fine. The websites suggested opening it up and removing dust that collects on the mechanism that cools down the CPU (heat sink? I’m not well versed in computer hardware, by the way). So, I did that. Now, I was under the impression that the mechanism which cools down computer processors was a bulky metal rectangular prism with deep grooves in it so that it can conduct heat away from the CPU and out through a fan. What I found instead was this copper coloured thing attached to a fan with 3 flat plates. There wasn’t much dust at all, so I took this copper coloured thing off and I discovered that the three plates were all covering one of three small rectanbles roughly 3cm/2cm. On two of those chips there was a gray muck, and the third was clean. I at first thought that this grey muck was dust that had accumulated and was not allowing for the chips to be cooled properly. I took a napkin and removed the muck from one of the chips. I decided to actually look up what this stuff was (which in hindsight I should’ve done before messing around with my computer) and apparently it’s actually supposed to be there… I tried putting as much of it back as I could, and then I closed everything back up. No, the computer turns on normally, runs normally, but it shuts itself off (overheats?) a lot faster than it did before. It may take now 25% the time to shut itself off than it did before, and once it’s gotten to the point where it shuts itself off I need to let it cool down significantly before it will even give me 15 minutes of use. It seems to work fine when it’s on my desk and I’m using it as a desktop.

So, my questions are…

1. How badly did I screw it up by removing that gray stuff?
2. Can I buy that stuff somewhere and just put it back on?
3. How can I fix the original problem of it shutting down after 2 hours?

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