I didn't ask what has been damaged, I asked what is being damaged. We've established that the CPU is not getting any hotter than it's running temperature, therefore it's safe. The heatsink will get a little hotter on average, but that's not going to effect it. The air in the case is going to get fairly warm, but everything in the case is easily durable enough to handle a bit of warm air.
What possible advantage will having manual control of the delay time using software give you in venting your case post shutdown; rather than giving a generous amount of time, say 10 minutes of fan time?
Now, if you're doing this, just because you want to, that's fine and dandy. I have no problems with that at all.
I'd suggest the Z8 Encore over the PIC as the uC of choice to start with. I wont repost all the reasons as I probably already sound like a Z8 Encore zealot to people here; just search for previous posts on it for the reasoning behind it.
The FT232 chip is a cheap USB serial converter that Jay mentioned earlier; You can use it to read USB with your uC. Drivers and specs are available on the site:
https://www.ftdichip.com/
If you still want to maintain your requirement #4, I'll go back to my previous post. The Analog Devices chip is the best option if you want to monitor fan speed and control it. I've played with directly controlling the fan speed and trying to read the actual fan speed at the same time, and it's very difficult. I never managed to get it working fully by just using the uC and some passives. I think the problem with it is talked about in some General Chat section threads.
Once you have those three chips, the uC of your choice, the ADT fan control chip, and the USB->serial chip, you have a full scale PC controllable fan controller with thermal feedback. It's fairly simple to program the uC to control the ADT chip and relay data and controls back and forth from the PC, especially if the uC has a hardware I2C block.