CAT 226 gettin' air in the fuel

I've tried everything I can think of,air will settle out over night,crank up runs smooth for a few seconds then starts skipping on no.2 and 4 and is full of air.I've resealed everything on the suction side,switched some injectors,replaced transfer pump,new head gasket,checked push rods and done leak down test on the valves......? I'm baffled,I took the injection pump and they re sealed.Let me back up,it all started after I turned the machine over,flipped up-right and let it set over night then had to manually get the engine to turn over.Once it cranked it was skipping on no.1,checked rods,valves etc. nochange,took the pump got it back on its missing on 2 and 4.

CAT 226 gettin' air in the fuel