Custom Server Case
Should be possible.
CAD software really helps when it comes to something like this, and Google Sketchup isn't a bad option, it just takes a bit to get used too.
I did something similar for a desktop I made for my brother a few years ago. It wasn't in a server form factor, but it was necessary, since it had a really weirdly shaped supermicro board inside.
Using PCI-e extenders saved my plan, since the GPU would've run into components on the board.
Also, another mistake I made when I designed it was a lack of airflow through the case. I had a 140mm vent at the front, which I used for a radiator later on, and a 80mm vent at the back. Some chips other than the CPU towards the back started getting really hot, since the motherboard was originally designed for a 1U server with air flowing over the whole board constantly. I ended up solving this by mounting several fans inside to blow on the back part of the motherboard where the other hot parts were, and added an extra 120mm fan on the bottom. Thankfully the hexagonal mesh on the front that wasn't for the 140mm fan kept it from being a complete disaster.
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