Okie, so lemme explain a few things.
1. You cannot add or remove items from the config, the config is auto-generated and auto-handled by the plugin.
2. I don't support custom items from plugins that rely on this mod because it simply isn't possible without rewriting my whole plugin to support it.
+ Doing so would make it hard to continue to maintain.
3. The problem you are having isn't with custom items, it's with custom Item Definitions.
4. You will not find any stack plugin that supports mods made with this plugin.