Most done with the latter. But the nice thing is once you have done it once it is much easier to keep things up to date and in sync from then on words. You can also peace meal it - setup one application at a time and migrate things one by one over to it.
painstakingly manually code every unique facet
That makes it sound a lot worst then it actually it. It is only a bit more effort then setting something up for the first time manually. And pays its self back many times over when you next need to reinstall or install a new system. Assuming you keep up with making changes to the code and not directly to your system each time.