- -

Looks normal to me. I don't think this is an issue.

The gateway generated underground, but did teleport me to the outer end islands when I threw an ender pearl in.

I don't think that's a bug; just a cave that generated underwater.

Can you elaborate? You might be able to fix this by reassigning key binds, using control+click to right click, and/or quitting and restarting Minecraft.

No, I brought him over from a village using rails (From 14w04 a/b chunks, newly generated)

Doesn't need to be a farmer, just as long as it's a plain brown coat (but yeah it is a farmer)