To make a short story long ...

So I have this 1050 john deere tractor in the shop with a yanmar 3 cyl. engine. Not something I normally fool with, special project for customer that does bring the stuff I normally work on. Anyway, this engine came in with oil running out of the exhaust manifold and blowing out muffler. Immediately I checked the turbo and it was shot. This tractor has something that looks like a coolant tank but the boost air travels through it, there is no coolant entering this tank apparently is serves as some sort of air cooler. This thing is full of engine oil. So I replace turbo and clean out the oil. Check the oil level and fire it off. It's running but smoking and skipping . Break off injection lines and number one is dead , but no fuel is coming out injection line at all until it reaches full throttle. And then it is just barely squirting. So I cut the tractor off and remove the delivery valve for 1. Every thing seams in order. Check the copper washer that seals the delivery valve, did not think that was an issue but wanted to make sure sealing surfaces were clean for reinstall. Install delivery valve and crank the engine with the injection line for one completely off. No fuel coming out what so ever. Loosen the delivery valve and fuel runs out of delivery port with nothing more than pump case pressure. Tighten it up, no fuel what ever. So I rev the engine, mechanical throttle by the way and is also the engine cut off, once again at full throttle a small amount if fuel dribbles out. I then throttle down and engine and the engine speed remains the same, so I start looking to see if the throttle linkage has somehow gotten disconnected. Then I think I hear the engine rev up some more but then again I am not sure. Then it it does it some more then some more, holy sxxx it's running on oil !!!. Since I wasn't prepared for this I did not have my air block off device, or know where it was currently residing, or have the air intake loose for the emergency shut off. So I grab a screw driver and remove the clamp that holds the air pipe to the air filter and remove it. The whole time the engine is picking up speed and I think its gonna blow with me standing over it, but I got I done and cleared out in time. Now I can't find anything to cover the air pipe, I think about removing my shirt and stuffing it in the pipe , then I find a folded up tarp and stuff it over the intake. The engine started to decelerate and eventually shut off. After a big pinch of snuff and sit down break, I fire the engine off , with the shut down device in hand, to see if there was any audible engine damage. The engine sounds the same as it did before it tried to run, but I did not rev it this time. Back to to injection pump issue. I remove the injection pump and find it to be simple, although the number three metering rod pinion has slipped out of time I was able to figure out how to correctly time and reassemble the pump except for the position of the metering rod I have yet to wrap my head around. It can only go two ways 180 out from each other. That's enough for one day.