DEISEL MECHANICS/GOLF COURSE MECHANICS ONLY PLEASE?

I work at a golf course. I'm one of mechanics.I work with the mowers club cars tractors etc not golf carts but a few days ago someone flipped the sidewinder mower over. There is no visual damage done. It is a diesel three cylinder Kubota engine 2012 toro sidewinder. When it flipped I towed it back to the shop and cleaned out all the oil from the hoses turbo exhaust fuel injection and everything.now I don't know if the guy that flipped it tried to start it right after he flipped it back over or not...but I know that's the worst thing you can do science oil isn't settled down yet and it everywhere. I wasn't there yet when he flipped it back over right side up but I hope he didn't try to start it. Well after I cleaned everything up I put new oil more diesel and new filters. I started it and it started right up but the engine is knocking real bad.( forgot to mention that I also bled the fuel injection and lines like you should) but the engine kept on knocking even after I let it run for like ten minutes. Whitish/ light grayish smoke is spurting out exhaust the whole time its on. Its not a continues flow of smoke just spurts every time the engine knock maybe once evey two seconds if idle is all the way down. But I kept lookin at it and a found if I take off the middle fuel injection line it acts the same without it on...still starts right up but knocks and spurts smoke out so that led me to believe it might be fuel injection? Please help any input would be greatly appreciated thx