You can carve and engrave wood and aluminum with the stock machine. How convenient it is depends on how much you intend to do and how quickly you need to do it. I think 3D carving large wooden objects could get real tedious at a spindle speed of 5,000 rpm. If you are considering the need for a dedicated vacuum system then this would suggest that you're going to be doing a lot of wood work, in which case the speeder would be a good idea. Lots of engraving work would suggest the need for the high speed spindle.
Software depends on what types of shape you intend to carve and/or engrave and not so much on what material.
You can use the same computer for CAD/CAM but not at the same time as running your mill. The low cost compromise is a new, fast machine for CAD/CAM and a $100 used computer for the mill controller, the requirement is a low spec computer, just make sure it meets the specified requirements.
Phil