This site has hardly had any posts in the last couple of years. Finally, a really good question.
I have a couple of things to suggest.
First, about your problem when drawing from less than two sources. The problem is that air is coming out of solution on the inlet side of the pump. When you try to pull water from one source only, the velocity of the water increases and this drops the pressure. At low pressure, air in the water comes out of solution resulting in bubbles. Typically, these bubbles coalesce in the pump strainer and once there are enough, the pump loses its prime. For most pumps the strainer has a clear top so you should be able to see the bubbles in there. There is a simple fix. Just put in a pressure restriction on the OUTLET side of the pump. This will reduce the flowrate of water and hence the velocity. If there is a ball valve, gate valve or something similar on the OUTLET side of the pump, try closing it part way. You may need to experiment to find the setting which allows enough water flow without the air bubbles coming out of solution. Don't worry about damaging the pump by putting more load on the pump. Actually, the pump power consumption decreases as you restrict the outlet. Just don't restrict it so much that your flow goes to a trickle.
Second, you asked about a two speed pump. I am bullish on two speed pumps because when run on the low speed they produce half the flow but use only 1/8 the power (nominally). Go for it.
BAF