Managed to get my factory to reach 200 seconds per phylactery, but took a lot of repetitive building...
This module here produces 1 energized spark every 2 seconds, I made 4 of them just so it would be 4 per 2 seconds so 200 energized spark in 100 seconds, well beyond what would be necessary.
This module produces 1 astral sheet every 2 seconds, but you need 5 of them to make 1 Elemental Chassis, so I had to build 5 of this module, meaning 1 Elemental Chassis per 2 seconds, so 200 seconds to reach the 100 required for a Phylactery
This module here is slightly more unreliable, but it produces an Immaculate soul in like 3 seconds or slightly slower, but since you only need 50 of them, it's reliable enough that it hasn't failed yet.
My personal preference with setting up Air Pump/Refinery is to do 6 of them, and connect the outputs with big merger + merger, and then funnel that into a splitter which powers 2 disharmonisers. It's good because then the output of Silica and Liquid Curse is always enough to fuel either a disharmoniser or a refinery.
The biggest bottleneck is just the Elemental Chassis, because producing a single Astral Sheet requires about the same amount of work as producing a single Energized Spark, and you need 5 Astral Sheets to produce 1 Elemental Chassis...