Thanks. The small-form-factor forum is really useful. It contains a lot of different case designs to fit mini-ITX motherboards and components testing for SSF builds. Thank you for the pointer.
I do agree with the virtual assembly approach to sort out the spacing allowances in order to decide on suitable system components. Unfortunately, one needs the 3D CAD model of each of the built components, e.g. case, motherboard, water cooling system, etc. (Another problem is in the file format that one'c CAD system can import). I am not sure all component manufacturers will provide the 3D model of their products at present.