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I finally got a perfect run: A full-clear with 13 hearts leftover at the end!
That can only happen if you do not use any health refills until you've looted all treasure chests, picked up the gnome, and killed the Mine King and cleared out all mines.

It took many attempts, and more than a few... educated guesses? You'll need to take some risks to do this, but usually just inferring which squares are most likely to be chests without actually seeing the minotaurs.

I looks like you're running almost exactly double the factory I am! I've got 19 air pumps feeding everything and churning out a phylactery every ~33 minutes. After I made my first, I sat down with pen and paper and worked through a bunch of diagrams trying to figure out exactly what input and intermediate resources each elemental chassis/immaculate soul/energized spark would require, and tried to optimize.

The biggest trouble I ran into was making sure each ingredient would be made at the correct rate, because it turns out balancing 3 sentient meats to 10 astral sheets to 4 balanced orbs et al is really awkward unless you're fully scaled up, and I wasn't quite ready to tackle that level of parallelization.

Thus, my factory is set up in three sections, with excess liquid curse from my chassis and sparks feeding my souls. Yours is so much better organized than mine - I love how cleanly the layout lets you see what each section is making, and how well you're gathering your excess to send to the markets. Well done!