If you ran out of
fuel, then you most certainly need to bleed the
fuel system. We had a 1GM10 Yanmar. There should be two filters. The first one is separate from the engine and needs to be primed. Our old one you just had to fill up and get all the air out as you put the lid on. Others have a bleed screw of some sort.
The second filter is on the engine and it does have a lever
pump and a bleed screw. Open the bleed screw and
pump until only diesel comes out. You may have to bleed the injectors as well.
This doesn''t discount the possibility of fouling, but running out of
fuel generally requires a bleed to get things working again.
Gerhard