Re: Jandy Aquapure and Intelliflo not playing nicely...
The timer in the IntelliFlo is not capable of controlling anything external. You either need to use an external timer or rig a current sensing system to detect if the pump is actually drawing power or not. If you had an automation system, it would take care of things, but without that the simplest thing is to go back to using an external timer.
The flow sensor has nothing to do with the pump or the pumps wiring. If the flow sensor isn't working then there is either a problem with the flow sensor or the SWG control unit.
Losing prime like that means that air is getting into the suction side of the plumbing. It could be a very very slow air leak that doesn't cause problems on high speed, but eventually causes problems for low speed, or it might be something simple like the pump strainer basket lid seal not sealing properly.