The primary objectives are to make sure that airflow is not obstructed and electricity is only conducted where it is needed.

My first though is to slap a non-transparent lid on the case and call it good.

If you want it to LOOK good as well, you may need to spend some money on longer wires and cables that leave enough slack for routing along the case edges. You can then wire tie them in place. You may even need a different case to make really look good, as well as considerable time to locate longer cables and get them installed. Be aware that data cables that are too long may affect critical timing, and power cables that are longer may also need to be heavier guage. If the case isn't going to get a transparant lid, lighting, and not be shoved under a desk, it probably isn't worth the effort.