Well, that took a lot longer than I planned. The account merge is now in a state where old players such as yourselves can resume playing Legacy. So I'll leave it at that for tonight, there are many things I still need to add so I've hidden Legacy from the Hunted Cow site for one more day.

You can merge your account in to your Hunted Cow account now, and use it to login. There shouldn't be any issues. The following features are still not added yet.

Development Server is down until further notice.
Wiki logins will work only for non-merged accounts.
Old players have not yet been granted their banner for being around for this event.
Legacy accounts do not show in the Hunted Cow accounts page.
Legacy does not have its own forum on Hunted Cow yet.
The support link at the top has no category for Legacy yet.

As soon as I wake up tomorrow I will continue with this and hopefully make it far more awesome. You can hide the Hunted Cow bar at the top of pages in Options if you find it annoying.