PotatoRynn

I was looking at your project, thought I might give you some ideas.
If you wanted to go the magnet route as @James Evens suggested, this reed switch might fit the bill. Its small and compact, not sure what the effective range is though.
Another option would be line of sight, your transmitter could consist of an inferred LED, or multiple, and your receiver could be based around a phototransistor.
The receiver could look something like this (super simple to do btw)

This would give you a very narrow window for your rx/tx, and the range could be adjusted by the output intensity of your transmitter LED.
As far as power goes, I would use a CR-2 or CR-123A type battery, they have high capacity in a small package, they are rated at 3v, not 1.5v like a AAA's, so you would only need one.
 
Note: If you do decide to use the IR phototransistor, make sure the wavelengths match when your sourcing parts. I believe the one linked above is most sensitive to 940nm.
 

Follow either this or this.
 

When it comes to the ports, it'll be just like having a hard drive. So long as you have a free spot on the motherboard for SATA, and another cable you can use for the power, you should be fine. If you only have a hard drive plugged in at the moment, you should have 3 ports on the board open. I doubt you have a disk drive, but if you do then you still have two free open ports. (If you do have a disk drive, honestly I would just take that out and replace it with the SSD.) I don't know much about the mounting situation though, I know there's some mounts you can buy on amazon for around 5-10 dollars, but I think they're smaller than the usual hard drive sized trays.

Windows activation keys have typically tied themselves to the motherboard. Even if you were to change motherboards, you can just reactivate Windows on a new board without a hitch most of the time. Cloning the OS does not usually mess with Windows activation. 

I decided to turn the fan down to "silent" in the bios, the temp at idle was around 28-35, something like that, and during load it was good too. I'm gonna hold off on getting a new cooler for now since the thing isn't crazy loud anymore. Thanks everyone for all the feedback, good to know that not everyone on the internet isn't toxic.