In your world building, not everything has to be plausible. With quantum computing not everything in the real world is plausible either. You have a lot of text that describes at the higher levels of how your biological quantum computer would work and however you want to break that out is probably fine.
For your quantum computer to work and be scalable in the real world - around 2000 a guy came up with what are now called the <PERSON>'s criteria. To paraphrase: 1. A scalable physical system with well-characterized qubit 2. The ability to initialize the state of the qubits to a simple fiducial state 3. Long relevant decoherence times 4. A "universal" set of quantum gates 5. A qubit-specific measurement capability 6. The ability to interconvert stationary and flying qubits 7. The ability to faithfully transmit flying qubits between specified locations
So for your question:
Q. What is your q-bit?:
A. Some type of iron containing molecule that has has at least two energy levels where an electron, or spin, or some other quantity can exist for a long time without somehow mixing its state with the environment. Since you are talking about magnetism - it is probably an electron spin, or an set of electrons in some sort of atom or molecule that are all spinning in the same way when they are programmed in some way.
Q. How do you program the initial state of the q-bit.
A. 855
Well, the details matter. Using 'spintronics' your can polarize the spin of electrons by sending the electrons through a thin layer of a ferromagnetic material for example making a spin field effect transistor, but since your alien evolved, I am choosing to assume that your q-bit molecules are in some kind of squishy biological matrix and little filamentary antennas structures in the brain are sending out short range RF pulses that set the q-bit spinning such that are spinning in the right energy level. The problem with this is that if the energy levels are closely spaced, I might have to have the creature operate at cryogenic temperatures, so maybe back to a spin FET like structure where little pulses of current might set up the spins the correct way.... or maybe something else.
Q. Long relevant decoherence times -
A. This and how fast you can program the gates is important tradeoff on how well you computer scales. If your molecule has closely spaced energy levels - thermal energy will make it unusable at higher temperatures, but maybe your molecule for some reason has widely spaced energy levels and is protected from interactions somehow so the state is maintained for some long (microseconds or milliseconds instead of femtoseconds or picoseconds) amount of time. The the problem becomes how do you program the molecule to be in the right state, and then have it interact or be coupled to another q-bit in a useful way.
Etc. Etc. the universal quantum gate, how information goes from the onely location to the other location are more related to the architecture of the quantum computer and details of how you would program it. For your biologically evolved alien, it may not understand how its brain works. (I don't think we humans necessarily understand how our brains work either).
So it is up to you as to what is plausible or not. But in quantum computing thinking about storage and algorithms can be quite a bit different than how we think about regular computers. BTW, there are non quantum computers like neuromorphic computers that are weird too. Ideas like registers, RAM, clocks and timing, can be a differentin these other types of computers. So a nanoprocesser is fine, but what does it mean? It is hard to tell. 790