Go into the filltypes folder to edit, then just add another line for your grain,
(<converter from="WHEAT" to="WHEAT" factor="1.0"/>) , for example,
you dont need GE, the fence will have a name and then the type of fence in the barn will have a name, if you switch them it should work. I did it once and got it to work but ive forgotten how to exactly.
animals dont show up in any pens, they're there just not visible, deleted the barn and replaced it and it worked fine.