I'm glad you're enjoying your stay here! I'll see what I can clear up for you.
The size of the model should be displayed in the right sidebar of the product page, just under the model availability settings and next to the material selector.
Markup is handled separately for each material, but in the new product inventory management, there is a "to all" button that will apply a single markup to every material. This is available in the "Edit my Shop" page.
I don't use the 3d viewer much, so I can't help you on those two points. Sorry
I've heard some people have had java problems with the 3d viewer, but as I said I don't use it much, so... If you're referring to the orientation of the model in the default rendering, that depends on the orientation of the saved file. If it's not showing up in the render... Well, I've never heard of that happening.
I don't know what you mean by the 3D "movie".
The default 3d render is always white. If you want to see it in a different material, for now the only option is to render it yourself or actually order it. Maybe Shapeways will offer more render options someday, but for now white is the standard.
Hope this helps!