Here a example.
I would like to remove the upgrades slots and the energy bar from the JEI Integration without changing the machine itself because i like the GUI like it is right now.

thanks for the mod anyways.

Now possible in Custom Machinery 0.4.1, see the wiki page for more informations.

Well, I can make it possible to override the jei recipe gui to not use the machine gui, and use it's own gui elements instead. And if the override is not specified it fallback to the machine gui.
I add that to my todo list.

Perfect. Hope to see that implemented!