The supposed upgraded missile, Song II, turned out to be weaker than the original Song missile created by the system, mainly due to the fact that system-created missiles have 100% energy conversation while the one he currently built only had like 45%.
Hence, while Alina focused on upgrading the missile, he was focused on the warhead.
The factory, which was upgraded to the maximum level before the exit of the system, has already the necessary equipment to create every type of weapon he could. The only problem is with the procurement of materials now that the mining system, unfortunately, didn't materialize with the factory.
Hence, Mark could only recycle the existing warheads lying in his inventory, increase the quantity of fissile materials, improve the efficiency of the implosion mechanism, and eventually increase yield. But, that also decreased the energy conversation rate in the process.