Maybe I'm not being clear about the fan.
You see if your computer controls the fan, it gauges the RPM. A new, well behaved fan might maintain a good RPM without much noticeable effort. As it wears out and get dirty inside, it slows down and is more difficult to turn.
The computer sees the RPMs drop and sees the system temperature and decides to throttle it up. This would make it seem like your computer is hotter and working harder than normal, when in reality your fan is just slower and having to work harder to keep the RPM the motherboard is requesting.
Regardless, it would be a serious mistake, imho, to put more money into this system before a) you know what is really wrong, and

whether not it CAN be upgraded to work well with Vista.