tigerdude426,

It should not affect the cradles at all but you may need to move the pump to the boxes rear.
I have no real knowledge that storing a sealed dry cell on its side does any harm I’m sure it make little difference. I have two batteries in my box just sitting in there no padding what so ever has been fine for years. If I was you I’d find a way to punch some holes in the divider so it can still vent on out the vents in the front and put them under the panel as they should be. A Dremel with a right angel cutter and one of those side cutting bits would cut some nice slots in it quick and easy.