By spinning colonies, you create artificial gravity. Shielding with time can come cheap with graphine or some new super ceramic material. In my stories, I will go into detail how these colonies like the O'Neill cylinder is built as I see how.
We need new vehicles like the worker pod from 2001: A Space Odyssey or even the Ball Pods from Gundam. With huge sections built in space, each land or glass section is slid into place. After every few sections, a bulkhead can be built or the main bulkhead is built and slid forward with progress of construction and in the vacuum is the terrain, infrastructure and such.
Farmers is some portions of the country are using food waste as fertilizer. It's non-toxic to the environment and I imagine any that wash into water ways will cause an explosion of the fish population because of the nutrients. With that said, soil is not a problem. Human waste can be recycled by either incinerating or recycling. With fusion reactors scheduled to go into operation within the next forty years, power is not a problem but the mirrors can still double as solar panels. In case of emergency, the panels can close to protect the 'glass' from debris or anything that can smash right through it.
Emergency shelters and life pods are a MUST in case the worst comes to worst. When completed, 500,000 to a million people pending on size can move to this colony and multiple can be built. As long as we avoid slamming one or two or three into earth, all can be well.
I take it you know all about Operation British during the One Year War?
Actually, the shielding would be inherent in the structure. The thickness of the metal necessary to hold the structure together is sufficient to prevent against damage from most objects. As far as larger objects, those would be attracted to Earth, itself, and it's unlikely any colony would be in the way. Even if it were, it would be detected at enough range to perform evasive maneuvers. Even the glass would be thick enough to prevent against damage from most meteorite collisions. The structure would almost REQUIRE a grid of several-foot-wide cells of glass, with steel/titanium supports between panels, so any damaged panels could be patched over, pulled out, and replaced, easily, and without major impact.
At the scale of the O'Neill Cylinder, 2 rotations every 3 minutes would generate equivalent to Earth's gravity in centripetal force. This speed is slow enough to prevent much note of the Coriolis effect.
The original design of the O'Neill Cylinder calls for agriculture pods on the large torque wheel at its rear end. (see the first picture) Personally, I find this unnecessary, given the scale, and clustered nature of efficient colonization. Instead, the same space could be occupied by solar panels, and agriculture taken place inside the colony, or, in further future, in entire cylinders devoted to agriculture, and shipped to residential or industrial colonies. Either way, the need for power is alleviated by having the massive array there. The torque wheel, as originally suggested, is large enough in diameter, that even at the mirrors' maximum angle, the solar array would be unimpeded. As yet, however, there is no solar cell reflective enough for the purpose of being a full-time solar mirror, as well as generating power, so, doubling up isn't possible.
Emergency shelters and life pods are inherent concerns, as this IS the deadliest environment. That's a fairly easy concern to take care of.
Through efficient recycling, the colonies can be self-sustaining.
