After getting the starter rebuilt and rewiring the engine to ABYC standards, tractor motor started up fine. It did, however, cough a little smoke when I revved it up. The smoke was black with a ting of blue. The valves didn't sound loud then but I figured I better check their gap. They were ridiculously off so I changed them after making my notes... figuring that and some Seafoam later would clear the carbon build up in the cylinders / valves area.
I agree... fuel injection timing doesn't just change itself but perhaps the needs of a farmer's engine aren't the same needs of a sailor's engine. No matter what, cylinder #3 is at TDC when the 1TC mark lines up with that bump.
As for dealing with this at the end, I'm pretty much at the end. All that's left is changing the transmission dampener & adapter at the flywheel, paint and an oil change. - D
PS The M25XP was pretty much given to me. The tractor motor I bought / traded for with a bunch of other stuff.