You want nice clean and fresh honed bores if you re ringing an engine.. If you don't, it will never bed in.

If the rust has penetrated to deep you may need to bore it out.

Regardless, to do it properly the whole motor needs to come out, and totally cleaned, all oil galleries flushed, oil pump cleaned...etc after the hone or bore/hone has been complete

And if your doing that, throw a set of bearings in it to.