So, 

 my first concern is to create compartments that are resistant to weather. So I need to fill in all these holes. I taped off all the holes and I will do a couple layers of fiberglass. Hopefully I can get them thin enough the battery still slides in but all the holes are covered without any gaps all the way around.

First I tape the inside of the area up to make the enclosure....

Tada, it is just masking tape.