I had the same problem in my VAIO. The reason sppeedfan reports no speed for fan #2 is that there is no such animal; just a CPU fan. This is where the problem lies. Actually 2 problems. Over time, the exhaust from the fan accumulates dust inside the box where the fan blows the hot air out. The second, I suspect larger problem, is that the thermal paste SONY uses, to put it blumtly, sucks.
You need to remove the cover from the laptop to get inside but this wasn't as bad as IO thought it might be. Lots of help here on the web. There are about a dozen small screws, just don't lose any.
Once that's done, you need to remove the fan/heatsink; another dozenish screws. You will have already bought: Arctic Silver thermal compund and cleaner ($12.99 at Amazon). Follow the directions and use the cleaner and surface prep liquids to thourouhly remove the old compound between the copper heat sink and the processor. While the fan is off, use the brush attachment on a vacuum cleaner to remove all the dust accumalted at the exhaust port. Now apply the Arcic Silver, sparingly (a dab'll do ya), reinstall the fan/heatsink, put the box cover back on and and be cool, VERY COOL!