Stop, when you are sure it’s safe to stop. Set your pre-capture time high in Cubase (I’m on 9, but I think that feature is pretty old, you’ll find it in the preferences), in case you’ve accidentially stopped you’ll have a buffer.
Probably less is more with orchestra. Basic EQing and some volume rides when necessary. Before anything see what you can do in terms of phase alignment by moving the tracks around a few samples or milliseconds.