I'm not an engine builder, but have rebuilt a few, can't see where mis-alignment of the jugs would cause any problems being the pistons are on wrist pins. I have to side with the improper measurements group or contamination from the oil someplace. Maybe heat issues?

 

You talk about engine builders having a bad day-------------years ago I felt rich and thought of hiring a major engine builder to freshen up my blown alky kb tractor pulling motors ------he had a dyno and I thought that might be interesting .We were there when the first one went on and they fired it warmed it a little and I then told him to shut it down becuase it didnt sound right--------they went ahead and took it to the limits of the dyno and it started shooting ducks and went down.they pulled it off put it on my shipping cart stuck the other one on and it ran right.I looked around and the bad one was loaded and I threw a fit ----------come to find out they had the pistons in backwards and bent the valves and messed up the valve train.I learned that day even the big boys mess up and turn their back

 

Put some kerosene in the bottom end and slosh it around a little, then suck it out with a turkey baster, etc. Then take a small shop magnet and fish around a little bit and see what you get. If it's clean repeat the rinse and magnet once more. Don't forget to flush or replace the oil lines too.
It's really almost impossible to get a cylinder on crooked as the spigot aligns everything up!!!
John

 

thanks, John!

precisely the idea i had!... will update once job is done