When I rebuilt my tractor deck I blasted, used self etching primer, then some bedliner paint. I'm a couple years into it now. So far so good! Only cost about $50 including blasting media and a couple cans of paint (all the paint was the kind you get in spray cans). I also got a couple heavy duty garbage bags and made liners for the boxes. I used a mylar tape to seal the seams (don't forget drain holes!).
I can't claim any credit for the battery boxes - I bought the new powder coated ones...and then added bedliner paint inside!
If you are repairing boxes that are not too badly damaged, grind/sand away the rust, paint (POR15 has had good results from many on this list, I have no
personal experience), and add a liner. A structural repair may be needed if the attachment area has been too badly damaged. Be sure to paint the new metal.
To prevent further corrosion, it depends on how badly your batteries leak. I believe some auto stores sell a mat to go under the batteries that will neutralize acid. Maybe that would help.
From: Andrew Poush
<agp vt edu>
To: Elec-Trak Elec-Trak List <elec-trak cosmos phy tufts edu>
Sent: Monday, July 15, 2013 5:52 PM
Subject: (ET) Battery box corrosion