How do I order a custom motherboard?
I'm studying computer science too and I'm hoping to learn to do what you are talking about. Over the winter break I made a 48x16 LED matrix with a little ESP32 single board computer. I don't know if I'll be able to do it, but I eventually want to turn my breadboard version into an actually printed PCB after I work with it a bit more. It's WAY WAY simpler than a motherboard. I'm learning Fusion360 so that I can build a proper enclosure and design the board. There is a picture of what I built below. It was a ton of fun and I love doing this stuff.
I'd recommend starting with something like that. Get one of those Arduino kits off of Amazon or you can start with an ESP32, it's basically the same, an esp32 is more powerful, but in the beginning that doesn't matter much. The Arduino IDE is pretty simple to start with this stuff and it works with ESP32 as well. Even if you don't have the money to do that, checkout tinkerCAD. It's a good place to start learning 3D modeling and circuit design. Last year I made this circuit as well as this 3d model that would theoretically be the circuit. That was basically what the entire class was about, making that circuit and making that 3d model and these are about as simple as it gets.
My point being, people get paid a lot of money to do the type of thing you are talking about, and it takes a long time to learn to do it. As you see in some of the other comments it's hell of an undertaking, however if you want to do it, YOU CAN. It's just a longer process than you seem to be expecting. There's nothing wrong with that, just start at the beginning and move forward. I find it super fun and building that silly robot was a blast, as was this matrix. Check out some TinkerCAD videos and find a project to build and go for it. Maybe you can follow a project in tinkercad then buy the parts and actually build it. Just trying to encourage someone to follow through with their interests! Get at me in a few years when you build your motherboard.
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