I'm starting to get the same feeling Fin. I shut the pump down at the first sound of it drawing air, which may have only been an air lock or something in the lines as this was the first time I had run the fuel system. I set the pickup as low as possible in the tank when I closed it up. Here's an excerpt from my log:
"Installed the fuel pickups into the tanks, ensuring they were in the right position prior to sealing through the use of a borescope through the fuel level sender port. Once this and the inspection panel was sealed in place with proseal, the fuel level senders were installed, again with proseal around the sealing face and the screws. #8 NAS1351 cad plated cap screws were used instead of Philips head screws so that future removal would be possible."
I posted on another thread regarding the Van's screens I am using (see link below). I think I will pump the tanks dry and check again the remaining fuel.