I don't see how you could possibly be collecting much water inside the hull with the hatches both on like that??? That's weird. Are you sure you don't have a crack in the hull at the seam somewhere? Anyway, I guess auto bailers might help.
BTW, looks like a triangular opening in the hatch on the carb side of the front cowl...is that just a decal or is it a real opening? If it's an opening I would block that off ASAP before it lets water straight in to your carb and cause problems. Open pipe side more, close off carb side.
One thing to try is to tape the front cowl seam, front to back on both sides, especially the carb side. The T-bolt doesn't really have an inner lip around the cowl opening to stop water from creaping in. Taping it and doing a few runs will let you know if that's where it's all coming in. This is where it comes in at launch and at end of run or stall...and when in someone's roostertail.