I reckon Phunk's right on the money with the pinion angle...... It's critical that when you set up a pair of variable angle couplings (in this case your uni joints) that the angle between the drive shaft & input end (gearbox) & output end (tail shaft) are the same.... It's to do with 2 different rotating inertia values & stuffs up your uni joints REAL quick if you don't get it right..... As per your vibration!
You could maybe sit something in the back of your ute to simulate the rear springs under load & then measure your gearbox to driveshaft & driveshaft to diff angle. If they don't match up you may have to cut & turn your diff mounts........ The shims might work though