Edit: Well I'm late again. (30 minutes isn't bad)

It's always a PITA Danny. (not as big a PITA as the Ujoint boot replacement, and the trick with that is to use spray silicone and fold the lips back on the bigger end that goes on the swingarm when installing.)
The advice for the shaft is to lift the swingarm up level (maybe tie it up), so the shaft is making a straight(er) shot at the ujoint. Twist, stab, wiggle, repeat. (same advivce on installing the boot)
And find a short stool so you can sit while fishing around for a while.
This was a very nice link with step by step pictures of rear end service and assembly that I actually printed out years ago. It's now disabled, but maybe one of our computer gurus can find it on a Wayback Machine thingy. Each picture enlarges nicely when clicked.
http://www.rattlebars.com/mtz/ujoint.htmlAnother piece of advice from this forum (Ricky-D)
Most damage to the bearing cup can be attributed to bad mechanical practice.
Namely allowing the swingarm to come to stop (bottom out) after removing the rear shock absorber bolts.
The edge of the cups are extremely fragile due to the machining for the seals.
Many threads have warnings about supporting the swingarm when disconnecting the shocks.