I had to change the text file syntax to get mod items to work.
Machine,Input_ID,Input_Dmg,isModItem,Output_ID,Output_Dmg,isModItem
Machine is now the name of the machine with a capitol at the beginning, so...
Macerator
Extractor
Compressor
... are valid machine names.
This is a working mod recipe:
Macerator,1001,6,true,1,0,false
This makes RP2 nikolite into stone. I'm still missing the output stack size, but I'll get that added in there.