Old house, new circuit, foundation penetration?

I have a 160 year-old two-story frame farmhouse with a round stone foundation and basement, a large sill beam, and aluminum siding. I’m planning installation of a split system heat pump, and I’ll need one or two holes through the foundation into the basement for conduit and Freon lines. I want to protect both the historical and structural features. Should the holes go through the foundation or the sill beam? And for the outside wiring run and shutoff, should I be thinking conduit across the exposed foundation, or an outdoor channel across the siding? Please, only answer if you’ve done something similar?