First of all, the best place for the check valve is on the end of the droppipe with none anywhere else. Assuming both wells have droppipe and footvalves, I recommend changing both to good brass footvalves. Get rid of the one at the pump, get rid of any fittings that aren't absoluletly necessary in both suction lines. (This reduces air leak possibilities) Most folks don't realize how such a little amount of air can really screw up an otherwise good install.
I would also tee the two wells together if possible. This will give you more water with the one pump and it would help you get rid of those valves that are probably sucking air through the packing nut. The pump will pull the same on two wells as it would one and get the water from where it can.