I'm not arguing, I agree. I had a similar instance, mine were all over the place. I don't see how in the world you can fix it with a tune, but I does work.
You put an amp clamp around the starter wire and use a graphing meter and crank the engine with the fuel disabled and watch the amp pattern. The weaker cylinder causes less load on the starter and the amps won't be as high on that cylinder. If they are all smooth you're good, if you have one low you pull the easiest to get to glow plug and use the firing order to figure out which one is the weak one.
There was many issues with his tuning. To the point where I said screw it and went to Tony. Best move I have ever made. Its a nice feeling having a tuner spend time getting your tunes dialed in a timely matter.