I finished up FactorioChem yesterday and really enjoyed it! It was certainly a different take on creating additional layers in an overhaul mod. Some of my viewers thought it seemed quite difficult, but I think by breaking the problems down into small parts, it was quite an enjoyable and achievable puzzle. I do have a few ideas to share.

-Could the specialty machines show their recipes in Alt mode?
-Sometimes Q doesn't work to pick specialty machines from inventory when trying to grab from a ghosted entity. I couldn't figure out a way to replicate when it works and when it doesn't.
-Would it be possible to have a GUI that remained open showing a particular molecule that you are trying to make? Especially in the later sciences, the more complex molecules are harder to remember what goes where and having the molecule open on the side would be helpful. In addition to that, the bonds are sometimes difficult to see, so a bit larger image would be helpful.

I am impressed with the mod as is and am curious if you have plans to do any additions or changes. Thanks for the work you put into it!

-Could the specialty machines show their recipes in Alt mode?

The thing is, there aren't actually any Factorio recipes for molecules, each conversion is done in Lua code. A single machine entity can easily have a conveyor belt in with various different inputs and produce different outputs without removing it from the ground. Especially the sorter.

The only thing really available recipe-wise is that the buildings show the kind of building that they are through their fake fixed recipe

-Sometimes Q doesn't work to pick specialty machines from inventory when trying to grab from a ghosted entity. I couldn't figure out a way to replicate when it works and when it doesn't.

I assume this is likely due to the settings object that spawns with it at the same position and size, getting selected instead of the building entity. I don't know if there's a great way around it without resizing or repositioning the settings entity, although maybe sticking it slightly north would z-layer it behind...I'd have to look into it

-Would it be possible to have a GUI that remained open showing a particular molecule that you are trying to make? Especially in the later sciences, the more complex molecules are harder to remember what goes where and having the molecule open on the side would be helpful. In addition to that, the bonds are sometimes difficult to see, so a bit larger image would be helpful.

That'd be helpful, I'll have to think about that as well

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Don't know if I'll get to these any time soon but I do think they'd be helpful

-Would it be possible to have a GUI that remained open showing a particular molecule that you are trying to make? Especially in the later sciences, the more complex molecules are harder to remember what goes where and having the molecule open on the side would be helpful. In addition to that, the bonds are sometimes difficult to see, so a bit larger image would be helpful.

Done :)

-Sometimes Q doesn't work to pick specialty machines from inventory when trying to grab from a ghosted entity. I couldn't figure out a way to replicate when it works and when it doesn't.

I found out why this is: if you copy and paste a ghost of a machine, the settings object that was previously behind it gets layered on top. If you copy and pasted that, the machine would be on top again and be pipette-selectable again. I added a workaround in 1.1.1 where if they get in the wrong order and you select the settings object, it'll look for a machine at the same place and pipette-select that instead. The "error you don't have the machine" sound will still play but it'll find the right machine to put under the cursor.