The first one is just for show
Now, the first thing to do when undertaking any major project like this is to be prepared to call your first attempt a 'prototype'. It sounds way cooler than saying you mucked up the first one, plus it looks like you planned it that way all along.
So here is my first attempt... err...prototype, demonstrating some of the ideas put into practice and then quickly scrapped because I realised it was over engineered.
First, we see the cheap-ass case from the local hardware store, looking pretty until Andrew gets his hands on it:-
Templating the IKEA motherboard tray was a good idea, it meant the holes lined up.........but could have been easily achieved by putting the motherboard on top and simply penning through the holes of the GIGABYTE motherboard...
Templating the fan holes; again, a good idea, but a slightly over engineered approach.
I'm still haunted in my sleep as to my decision not to place the PSU where I had templated it in this picture...
Here we see the IKEA motherboard tray sliced and prepared for mating.
Later I counter-sunk the holes at the back to allow use of nuts and bolts to hold the motherboard on. This was over engineering.