I'm naming my animations the same things, however, they still overlap. My older monsters have same name animations don't overlap though. It doesn't affect me that much right now, but it could look really weird on newer monsters.

In 0.2.8 I've removed the same-name system -- this was a last-minute design change so that animations and emitters are more consistent with other types. They now all have the same activation rules, so instead of using the same name, use the same (non-zero) group number to prevent overlapping animations.

Monster animations made before 0.2.8 are automatically converted to this new system, so if you were to change their names it would have no effect.

I don't see anything for groups though. If you mean modifier groups, how do I stop the original body and the new body from overlapping?

Yes, it's what used to be modifier groups. They're now better understood as 'activation control' groups, where each item has it's own activation controller that works in exactly the same way. So, to stop the new body from overlapping, just give its activation controller the same group number as the old body (and make sure the group number is not used by something else).

To convert the old animation automatically, I generated group numbers from the label, and 'body' comes out as 585. So all you should need to do is type 585 into the new body animation's activation controller group.

Hope that makes sense! I'll try to make this a bit user friendlier at the interface level later on.

Alright, I changed the group numbers to 585, but that didn't work. What confuses me more though is that the old monsters don't have anything like this, but seem pretty much the same.
Anyways, I've come up with something different, I just took a modifier called neutral, put it in the same group, and set it to a parent_active trigger. It seems to work.