First, you've got to realize that you're making several very bold assumptions given current physics: (1) that we can build O'Neill cylinders with current or future materials that resemble anything like sci fi expects (probably not -- pressure vessels are hard, mkay). (2) that we have a means to accelerate something larger than a probe to a significant fraction of light speed (this is actually the least difficult problem, but I suggest you look at the energy and travel time requirements). (3) that there's any conceivable way for this thing to stop upon arrival (much harder problem without magic engines).
If all of the above are reasonable, then, well, you bootstrap manufacturing in situ in the asteroid belt or in a planetary ring or whatever. Not a huge problem. You obviously need to target a second or third generation solar system in order to find metals and heavier elements on arrival, but that's trivial if you've solved the "stopping upon arrival using the energy and mass you brought with you" problem.
If you could send very small self replicating factories that could take their time to arrive, and upon arrival built a huge laser array used to slow down your larger shipments as they were inbound, you might be able to pull it off... With a few thousand years of preplanning. ;)