I have the same question as to how the Aquapure should be wired with the Intelliflo. Right now they are wired separately and the flow light is on even when the pump is turned off. We have not started chlorine production yet as we want to get this rectified.

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.

OK understood about the wiring. - If the pump is off then the flow sensor should shut off the chlorine production. The flow led should not be lit and the lcd display should read "no flow". Do I have that correct? Right now when I turn off the pump the flow led stays lit and the lcd reads "flow".

That means your flow switch is not working, which is dangerous. You don't want the SWG to ever be active when the pump is not pumping.