fuel pumps

It seems that you need to first confirm if the problem is on the suction side or pressure side. If it’s the suction side, then the expected problem would be fuel vaporization from the low pressure created by the suction of the Rotax pumps as we have been discussing.  I don’t understand the erratic amp draw of your boost pump. I would think the demand would be quite constant. I don’t know of a pump that would give you a pulsed amp draw like you are describing….but I’m ready to be corrected on that.  This needs more investigation.  

If the problem is on the high pressure side, the places to examine would be the fuel pressure regulator and the fine filter.  I don’t know the placement of your fuel pressure sender, but if it’s downstream of the fine filter and there is no bypass around the fine filter, then a partially clogged filter would give you low fuel pressure and it may be improved with a second pump running. In this case, you would expect to have very little return flow back to the fuel tanks since the pressure regulator would be closing off the return flow trying to raise the pressure.  If you have a healthy return flow, but low pressure, suspect the fuel pressure regulator.   

Since this situation seems easily repeatable, then you or your mechanic should be able to use an analog fuel pressure gauge temporarily placed in various positions in the fuel system to isolate the problem.