First, you should know that computing is done with electrons, not nucleons. That means the fundamental limit is at a length scale of the size of atoms (i.e. electron orbits) and not nuclei. Atoms are about 0.1 nm in size, whereas nuclei are about 0.00001 nm = 10 fm across. That's a difference of four orders of magnitude, so it's pretty important.
Second, your intuition is off. The jump from "being able to manipulate X in a laboratory" to "being able to build useful devices with X on a large scale" is large. We've been able to handle individual protons and neutrons with the right equipment too, but that doesn't mean we're close to building computers out of them.