What type of pump are you running. Had a similar issue when I went from a noisey old Facet pump to a Holley Red fuel pump. Ran fine until it got a bit of air in the pump. Would coast to a stop. Had to suck fuel through the lines, hook it up again and off I'd go. Got old real quick.......
Went back to the old Facet pump and didn't have another issue, except for the noise.......