I've mostly fixed this issue, though it's hacky and really poorly done in general. It was 3 main steps:
Extracting the mod into its own folder to work with the \prototypes*.lua files.
I went through the files. In all of them except technologies.lua, wherever an icon was listed, like for example, icon = "Advanced_Machines/graphics/icons/advanced-electric-furnace-icon.png", I added on the next line below it: " icon_size = 32," (without quotation marks.) In technologies.lua, I changed icon_size to 128.
I then went through the recipes, and resolved the Alien artifact issue, by just deleting any mention of Alien science packs in technology.lua, and in recipes.lua, removed any reference for alien artifacts.
Lastly, I went back to entities.lua, and "fixed" Voldkost's issue by removing the section labeled "working_visualisations = " as it was causing that issue he has screenshotted. This means the advanced chemical plant doesn't do any fancy animations, but at least the mod somewhat works.
Was any of this worth it? Who knows anymore, man.
Dawolf, please fix your mod.