That kind of nanotechnology (Von Neumann Probe style) is beyond any limits of the kind you allude to. It can remake a whole biosphere, change the chemistry of the atmosphere, and (eventually) not only change the oceans but change the presence of oceans.
Actual limiting factors:
atoms of the right types readily available. C, H, O, N, P should be no problem. Even without metals you would rather grow buildings out of organic molecules anyway. Small quantities of various elements are crucial for catalysts and special organo-metal complexes that do interesting things.
energy. The natural biosphere uses solar power. Advanced power could be used in local areas for specific industry. Fusion would require a lot of infrastructure before being possible.
executive intelligence and memory. Storage might be tight in the "seed" probes, but that could be supplemented with transmissions. After setting up a receiving station and growing lots of memory, it can download extensive plans that follow via laser.
Note that without nanotechnology, detailed plans for self-reproducing probes have been analyzed in detail and published (and this one) (etc.). Nanotechnology changes nearly everything, but you can get an idea of the kinds of planning needed.
Some miscellaneous thoughts: the seeds would be traveling quite fast, so how do they stop? Final landing can use aerobreaking and a large craft break up in to individual small seeds. But some executive control, archiving, and even heavy industry could be on an airless moon. If that's the first stop how do you stop? If the atmosphere is the first stop, how do tiny dumb seeds boot up enough intelligence to plan enough industrial complex to build rockets?
Tiny seeds will be dumb. They can start mining and collecting materials through vine-like growth, but what about planning? Maybe a larger seed unit would be necessary, with very dense and durable memory on board.
Basically the more bootstrapping, the more difficult. Keeping a functioning command unit in orbit from day 1 and sending down seeds with directed landing sites is far easier.
Such a "large" probe is still smaller than a colony ship, and not limited to acceleration levels. Slowing down can use a magnetic parachute, but is that enough? Retro-rocket reaction mass can double as shielding during transit.
Now if technology can do that, why send bodies? The original slow-boat colonists might arrive to find the world inhabited by those who beamed themselves over, or by intelligent machines who built the place.
You could probably have a whole series of stories about different seed destinations and how things went wrong on each one!