If you have 1 kW universal nanofactory, the minimum estimate of the amount of time to produce, say, a sturdy steel shovel (or a pound of rice for that matter) is around an hour (one erased bit per atom at Landauer limit at room temperature and no other energy expenditure). The more realistic time is probably around 1000-10000 hours or a month to a year. Diamondoid shovel will be lighter (and can be built faster), but there still are limits on how light it can be (and you can't make lightweight diamondoid food). Rice that costs 1 - 10 megawatt-hours per pound is hardly sustainable.

Universal nanofactories are quite energy hungry due to amount of computations and operations required to place individual atoms.

See part 8.2 of http://crnano.r30.net/Nanofactory.pdf for example.

So I think that universal nanofactories will supplement instead of replacing traditional manufacture methods.

Specialized nanofactories can be more efficient (e.g. biological processes), so a nanofactory that churns out rice at reasonable energy cost (less than megawatt-hour per pound) is realizable, but not so versatile, apparently.

I'm sorry to rain on your parade, but it seems you need access to a megawatt-class power source (that's around 140x140meters or 460x460feet of solar panels) to enjoy a universal nanofactory which is not painfully slow.

Atomic "lego block" factories will probably be a suitable compromise: higher speed, less prone to abuse (building toxins and poisons, for example).