Makoman
"Hermco" would be the guy to ask for advice. You need to get those batteries above the deck!!
But here is a couple ideas you could do and still maintain your floor configuration.
The original floor scuppers were glassed in. The floor holes were sleeved 90* out thru the transom
Before I enclosed my transom, I built a gutter system by spliting PVC pipe in half and glassing it around the inside edge of the deck hatch.The water run-off was funneled to the floor scuppers.
The only problem here was the floor hatch had to be modified so it fit tight against the splashwell. You will see in the picture the "curve" to the back side. Then the hatch was hinged to the splashwell.