[lineslinger]

Do you know the interior set up of your tank? Is the pickup point in a baffled chamber or is it just an open area, with no enclosure to contain fuel for pump demands. Another possibility could be the lack of a properly vented fuel tank, losing your pump prime due to a vacum building within the tank
As your fuel levels get lower you could lose your pump prime due to sloshing during braking or cornering, or as you thought vortexing down through the pickup and allowing air into the pump thus losing your prime. I am not familiar with the construction of an EM fuel tank but you may want to contact the dealer and hear what they have to say.