Everytime I try to upgrade it, it just eats the core and then tells me i'm missing items. Not sure if I'm supposed to progressively upgrade it or not but either way this is buggy as it deletes the core from my inventory everytime I get a new one and try again.

Console output when I try to upgrade with everything in my inventory: https://pastebin.com/VDtFsppB

Looks like something I missed during the 1.11 port.

You don't need to progressively upgrade. The issue was caused by the core vanishing.