I created a pull request for the breeding and enriched rods and did some more math on potential breeding setups when going with 10_000 Neutron Loss and 4_096_000_000 Neutrons Required. Overall the numbers seem very reasonable, requiring what some would consider a constant nuclear explosion worth of neutrons, quickly eating through fuel rods, however outputting ~5 Enriched Naquadah Enriched Rods per Pu-239 Fuel Rod in a matter of hours.
It is fairly straightforward of a processing chain, however much more difficult compared to just getting plutonium as a byproduct from ore processing.
Making the 1x1 reactor more expansive wouldn’t fix any of its problems. It is only mildly more powerful than the 2x2 reactor (allowing higher moderator rod outputs, but the neutrons are not “free” anymore with the “new” neutron maximum system, however much worse for breeding as double the neutron loss would be applied with the “new” breeding system), its most powerful feature probably is being easier to automate than the 2x2 reactor. The issue with the 1x1 reactor is that is simply behaving in (for users) confusing ways with moderators and breeding, resulting from how it is implemented.