We have reasonably good prototyping tech that could be adapted to produce replacement parts for many items.
I think this is a misconception, and probably the one that is most likely to make a generation ship impossible for some time. So many things have no simple method of manufacturing at a small scale. Computer chips, optics, any chemical process that's not 100% reversible (which, from an engineering standpoint, is all of them). Also, you have to keep in mind that many prototyping techniques simply aren't as good as traditional methods; you can 3D print a new bushing or o-ring, but if that replacement isn't the right kind of PTFE or Viton is it really worth it? And what happens when the prototyping machine breaks?
Unfortunately, you always need spare parts and materials. Determining the MTBF for components and how to deal with spare parts is a huge problem for the Mars missions right now. The more complex a system is, the bigger the spare parts list become. This is so much of an issue, they are actually considering giving up on an oxygen generating system. The mass of spare parts needed for the air system is more mass than simply taking enough air with you.
For any time in the near future, the best way to develop a Generation Ship is to actually send a Generation Fleet, and have them cannibalize themselves (technologically, and probably literally, too) until there's only one left.