Can (at least) basic flight instruments be added to an acft that has a virtual cockpit provided with the model already? (or do the instruments need to be referenced by the model itself?)

At the moment, no. It needs to have a part assigned in the model. Of course, the AI aircraft in CFS2, had no VC at all, until a gentleman by the name of Bruce Thorson cracked the code a few weeks ago. So who knows what can happen?

The VC gauges are defined in the panel.cfg in the same way as for the 2D panel. This means that you can change or add new gauges. The only limitation is that you can add gauges only on surfaces defined as a panel in the VC model file. Best regards, Chris

That is also my understanding of it - the position & size of the panel itself is defined in the model. But the gauges selection and position (and texture of the panel for that matter) are held outside and editable.