I made an account just to comment on this game.
I curse you! I've spent HOURS and HOURS on this game!
I worked up to the phylactery, then back down, then back up to increase how fast I could get it.
I'm running 40 disharmonizers on air pumps full time. 30 go to gems 10 go purely to silica, the extra resources are all going to markets so hardly anything ever gets voided through abyssal doors.
I make one phylactery every 15 minutes, most of the waiting is silica powder and to solve this I need another 30-40 disharmonizers just for the powder which I will definitely do. 
Improvements I would like, mostly as endgame content:
-Blueprints as somebody said before (including connections)
-Mass move, I manually moved around SO MANY splitters/mergers (again including connections)
-Mass place/shift place so you don't have to go back and forth
-Pick up or delete machines
-Bigger splitter/mergers, with more ports, both in and out, this way more items can pass in a single tick (relevant) with big builds
-Overflow management, I made the thing where 1/128 of the items get sent to market until it is full but that takes up so much space and makes it really messy.
-Increase max zoom (zoom out)
-Selling price of items, once you have markets
-A way to move progress to windows version from browser. I went too far for my browser to handle before switching to windows.
Thanks for wasting my time <3 I haven't spent this much time on a game in a long time.
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!