Alright, I got that to work, but they still wont' combine with the flasks. I'm guessing there's a default name for those that I need too? I added "_01" to the end of the flask names thinking it might work, but it didn't work.
Edit: Despite the fact that I got the first combination to work, I'm now cutting out the salt mixture step and mixing the saltpetre directly with the the vitriol, and using seperate flasks for every new substance. (chemical container = saltpetre, cuprite = vitriol, calamine = ammonia)
Edit2: I've solved it by matching changing the in-game item names and internal names in the callback. They matched beforehand, but for some reason by changing them both to something else, the combination works now. Here's my script as it is for anyone else trying to figure this out.