I'm sorry, what?
What custom items from other mods are you referring to exactly?
Stack Modifier is designed and built to automatically handle items customized from other plugins like items with custom names, skins, text, etc.
You shouldn't have todo anything except add it to the server and use the UI editor to set the stack sizes you'd like to use.
Plugins like SkillTree recommend stack modifier to avoid it's custom items having any kind of stack problems.