Hi Victor,
I'll try to answer all the questions together as they should be all related to the mesh.
First, I was surprised that the "smaller" wheel mesh is around 10000 times smaller than the other one... I don't know why it's designed this way, but it leads to problems: If you directly use it, then it's too small to represent anything physically meaningful; Most of the 6 or 7 digits that you have presenting the XYZ of each node are wasted since they are used to store the mesh's offset from the origin (0,0,0), rather than the relative difference in spatial locations among mesh nodes. This mesh is probably yanked from something else bigger, but that doesn't mean you don't have to pre-process it to make it reasonable.
Speaking of scaling a mesh that is not centered at the origin: It will also enlarge the distance between the origin and the mesh. This is because the scaling function will just multiply the XYZ of each node---it's a very lightweight utility anyway. For example, since your mesh originally sits at Y coordinate being around 5, so if you want the mesh to appear in the simulation at Y being near 0, then the initial Y coordinate of the mesh must be -5; and if the mesh is enlarged 10 times by Scale, then you have to set the initial to be -50. You could correct the CoM (drag it back to 0,0,0) of the mesh by using Move before setting the initial location of the mesh, but I guess at this point, the easiest thing you can do is instead just re-create the mesh, so its CoM lies directly on the (0,0,0) point of your mesh.
Also you should InstructBoxDomainDimension to make sure your domain is big enough to hold everything you have in the simulation.
I suspect the many anomalies you observed are caused by the wheel being at unexpected locations and having unexpected sizes or shapes when the simulation starts. But all these you should be able to spot by outputting and rendering the system after initialization. Did you try that and can you show us if the initial status of the simulation looks all right?
Thank you,
Ruochun