I know what you want to do but:
If your going to use the mugen cover why not just use mugen battery or 2x stock put together
There are many ways to do this, the way im doing it is pretty easy to do, and i will try to make a guide if anybody is interested.
Another way is to just grind a little bit of the top of the plastic on the connector part of the battery and then making a connection from first to second battery just trough + & -, when i get more battery's ill try to make this mod

The thing you describe looks like you want to use the battery's so you can go from mugen cover and the nice original cover, but again this will charge/discharge your battery's uneven, should not give problems to begin with but as time goes one battery could be so used that it will not give anything extra having 2 battery's over the one good that remains.