Well, at least you got it running without scattering it. Sounds like there may be a big air leak or it is starving for fuel. Not familiar with the Yanmar injection pump. IIRC, Bosch pumps could move, similar to distributors on gas engines a long time ago. to set the final precise timing. Looks like all those little arm thingies may not be moving properly? Maybe time to take it to a shop for calibration. Maybe it is out of time somewhat?
Paul T