I really don't want to mess around with a higher voltage battery just for the water pump. If I do that I'd like to whole car to run off the higher voltage. I considered getting some Leaf cells to do this, but have since axed the idea since my lead acid deep cycle is brand new. Next time!
If your going with an alt delete I don't see any reason not to do it unless you don't have enough battery capacity. My commute is pretty short (7 miles), and my capacity is more than enough for a few more amp draw. If your water pump is pulling THAT much power, its all the more reason to get it off the engine and on to the battery IMO. You'll only see that much more fuel mileage because of it. If your water pump is pulling too much power, then its time for a smarter controller IMO which is why I'm doing the arduino controller. I anticipate this thing only pulling about 50W max.
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