I tried Tim Benson's suggestion and here's the result:
I couldn't pull the ball joint any further outward than that, but I still think it's an improvement. The universal now extends into the flywheel about the same amount as the other one does.
I think that's an optical illusion. I double checked and they're all installed in the same way. I also tried rotating them 90 degrees but they wouldn't fit that way.
It can't be done by hand, at any rate. I just tried on a spare motor and the flywheel wouldn't budge.
Regarding moving the flywheel on the motor shaft... NO you cannot do this by hand and should not even try.
Just pulling and tugging on it is a very bad idea, and if you are unlucky, you might pull the shaft through the armature and destroy the motor. If you do decide to do this, you have to use a wheel puller (NWSL "The Puller" will work).
But it seems like you've got it running well in any event.