Portal linking is based off of map coordinates. You can link up to a portal that is in the same area as you are but when you go back through you will always go back to the first portal that it was connected to.
About the cows at my place. I was the one that killed them. I was lagging at my residence so I started bringing the entity count down.
I may setup a separate animal pen a little ways away from my residence so that you can use them and they wont lag my slow computer down.
We have had a inactivity system in my old gaming group. We may be including something like that soon.
Villagers can be moved by minecart, but I need to disable the death by minecart feature. That is off now and you should be able to load them up when you try. I am in the process of making a vote for that so that you can toggle the feature.