I was also wondering if vessels should be had for the new Beasts (we'll keep the name "Chakra Beasts" for simplicity). Another idea is that they have a village seal that can only be unlocked by Elders (or whatever you want them to have, perhaps they have different hierarchies) when the need arises.

That was supposed to be read as a list of possibilities. We could:
A) Remove Lightning and keep the 4 "basic Elements" or
B) Add another Chakra (suggesting Metal, though it doesn't have to be)
Regardless of the route taken, the strength/weakness relations would have to be adjusted, which wouldn't be too difficult. We could alter it completely or even omit the fact that there are one's that overpower others, creating a level playing field and removing automatic disadvantages.

The reason I thought Metal as an additional Chakra type was only due to the Chinese idea of Elements, which are actually Metal, Fire, Water, Wood, and Earth and omits Air. 

I find it cliche to have inherent negativity between nations. That's what the manga has already explored in great detail. I don't much care to follow suit. Of course, the actual plot of the RP could be vastly different with a similar canonical discrimination.

I think, for now, we should just have a literary map and allow our minds to create the image. However, at this stage, it'd probably be best to cement the fundamentals of the world. Or would you like to "create" the map first?

Yes, please do!

Also, any thoughts on that last section of the OP?