I'd suggest a 2nd auto pump, on a different fuse, and even on a different battery if you can do that. We have boats left in the marina at work which require pumping out from time to time by the staff cos their pumps have failed or something.
My cover is all in one, but since the tubes are in water when not moving, putting the cover on the boat would result in the cover getting weeded up as well unfortunately.
We had very heavy rain the other week - recorded at 200mm/hr for a fair while, and unfortunately even on dry land my boat filled up
Turned out the trunk had kinked, and was only dribbling water out the back... which is fine normally, but this rain was slightly excessive, and managed to get in at the transom in pretty good quantities.
We've got a 500gph rule auto pump on the dory at work which is constantly open to the elements, and it's lasted nearly 2 years now - all we do is take the top off every so often and clean out the little sive to keep the water flowing. Removing the sive will let crud get in, and the pump blows fuses