About a month or so ago, I noticed that my computer started slowing down and the main cpu fan was running very fast and loudly. What does this mean and how do I fix it?

It means some process is running your CPU constantly.

Open the Task Manager > Processes and see what is using the CPU.

Check you CPU temps - make sure all case fans are spinning freely, and inside the PC is clean of dust, dirt, dog hair, dander, microscopic critters that eat dander, and the microscopic critter droppings they leave behind!

You need to check the temperature of your CPU, just download this program (free) and it will do the job.

I use speedfan on a couple systems and it works great. However, I prefer Motherboard Monitor. Sadly, since the author quit supporting it, the number of recent boards it supports is dwindling. He released the source code to an active user base and so it is worth checking to see if your board is supported. Alternatively, most motherboards and many pre-built computers come with a hardware monitoring utility that works in Windows too that will monitor temps and fan speeds and often various voltages too. It is logical to at least hope that the monitoring program that comes with the board is fairly accurate and already configured specifically for that board. For some reason, these utilities are often buried deep in the CD and you have to hunt for them.

Using a Windows based program is much better than checking the temps under PC Health in the BIOS menu - when in the BIOS menu, the PC just had the opportunity to cool down during the reboot, and looking at the BIOS menu is about the least demanding task the computer can be assigned. In Windows, you can check the temps when the computer is actually working.

The point remains, you need to check your temps.

I downloaded Speedfan. Initially, my fans were running at %40. I played with both speeds, up and down, and then closed the program. The fans all of sudden started running at %100 by themselves. I ran speeedfan again, adjusted things, set it to auto. As long as speedfan was running, everything was ok, but when I existed the program, the fans started running at full speed with a lot of noise. I ended up uninstalling the program to get rid of fan noise and high speed (yes, I set it to auto also, it did not work).

I think when controlling fan speeds through the motherboard fan headers, it is better to use the program designed for that hardware and provided by the maker. I only use Motherboard Monitor or SpeedFan for checking temps and monitoring fan speeds, not controlling voltages. Either way, it seems to be a hit or miss thing - your board is either supported, or not - and then may be not completely.