the exclude on the gradlew.build isnt working, models going on the flansmod.jar and bugging everything the shit out, fix it and change the .jar on the website that got the content pack models on it.

Works fine for me.

well my models were going on the flansmod.jar aswell, if you look at the download on the flans mod website it got the models from his packs on the main jar, that could make a lot of problems

I don't know why flan's upload contains the models but the script does not produce that problem.
If you added your model directories to the build script in the same way that the official ones are added and then cleared your build files then your models would also not go into the flan's mod jar.