welcome aboard, nice to see you here! And thanks for the great introduction.
I've just checked 'Marble Clock' and it is a beautiful and very interesting machinery indeed!
If I get you right you would like to simulate the mechanism altogether. Even if it would be possible it would require a lot of time to correctly define such a complex system than a lot of computaional effort to run the simulation. (I'm not sure that magnets are supported in SimScale.)
CAE - Computer Aided Engineering - is primarily on quantitive results of simplified models (stresses, deflections, temperature, pressure distribution etc.) rather than visualization of sophisticated complex systems.
If you are to design such a clock I'm sure that you will find SimScale a handy tool to check and optimize components by the way!
I suggest to check the Public Projects page first to have a feeling what is possible plus there are a lot of other resources on this site too. Of course feel free to ask any questions you have on the forum.