Add the following annotation to your IFMLLoadingPlugin.
@IFMLLoadingPlugin.SortingIndex(1001) // Magic value, after deobf transformer.
Change your IFMLLoadingPlugin's getSetupClass(data) method to:
return org.minimallycorrect.modpatcher.api.ModPatcher.getSetupClass()
Load your patch files with ModPatcher in your IFMLLoadingPlugin's injectData method. For example:
ModPatcher.addPatchesFromInputStream(MyClass.class.getResourceAsStream("/modpatcher.xml"));
See the example coremod for more detail.