They seem pretty easy to setup.  I am just trying to make all the fields in ItemFishingRod public.  Do I need to make a core mod and add the transformer there or I can I do it my regular mod? 

You can add 'FMLAT: "yourFile_at.cfg"' to your META-INF/Manifest

then, put the transformer config in the same folder.

This way you don't have to make a LoadingPlugin and a coremod.

That's what I did.  How am I supposed to use the private vars in EntityFishHook in my dev envourment? I extend EntityFishHook and copy the update method and change Item.FishingRod to my custom rod but all the cars are private so I can't compile.