Back when I was semi-seriously thinking about printing semiconductors, one of the issues which stalled me was figuring out how to put wires through the vacuum chamber without destroying its integrity.
I stumbled over one approach: http://www.douglaselectrical.com
No idea what pricing looks like at dev scales nor production scale.
I also have no idea about cutting holes (and cleanup) without wrecking everything. But I seem to remember some chambers come with holes already in them.