If you run out of fuel, you need to prime the system after filling up. Cranking for long time with gas pedal on the floor might work, but than you might need new starter or battery.
Read the manual. There is bleeding screw on the top of upper filter and loosening fitting on the injector helps. Do you have manual priming pump on your engine?
That engine is self priming, but it can take awhile. Sounds very much like a leaking O ring in the fuel system is allowing air in. Do you see any bubbles or leaks in the plastic fuel lines? Did you recently replace the prefilter and not also replace the O ring?