Use the metal cover that comes from the motherboard to mark where to cut.
Cut The case - Bottom
Cutting the case is an iteractive task. All the time you have to check if there's something jamming the motherboard. Try to cut as minimum as possible, specially the parts used to hold the case together with screws. For this project one mounting pole was sacrivfied leaving the other 3 to be used to hold the case.
Cut the case - TOP
With the motherboard was fixed on the bottom of the case (using superglued plastic hexnuts/standoffs) it is time to remove any plastic piece that touches the motherboard preventing the case to close. As before remove the minimum amount of plastic as necessary.
Compact little fella you got there. Nice job!