I went for what seemed like a good level of organisation:
Java
__________
Mekanism
__________
Minecraft
Forge
FML
__________
Netty
LWJGL
__________
Other APIs
__________
Static Imports.
Move Config variables into their own class, (in api because other stuff in API references config, may make sense to move it back to common later), and move Blocks and Items into final variables in their own classes. It looks a lot cleaner this way and my OCD can finally rest now.