After reviewing all of the build instructions again I found my timing issues and have been able to resolve them, yay!!
Initial Drive Assembly
During the build I had a couple times that the chains of the initial drive assembly broke and it appeared that when I reconnected the chains I did not keep in mind the correct timing for the four chains causing issues with the load shifter. This caused the bucket on the conveyor to hit the bar instead of neatly sliding into the grabber.
This even caused to occasionally tip over a bucket causing a whole range of other problems.
Bucket Unloader / Empty Bucket Mover
Combined with the issues of the initial drive assembly there was also an issue with the two parts that are picking buckets from the wheel and putting them back on it.
Buckets where sometimes pulled back a little when they were placed onto the conveyor belt. The reason for this was that the arm was not all the way down when it started to move back to the wheel.
After making this change the system only requires 20 buckets instead of 21 to ensure there is always a bucket available when the balls are being dropped by the ball loader.
Modification to the Spiral Lift
I also made a little modification to the Spiral Lift module. I found the base to be too weak, it is only supported in the middle. I added four pillars to it, one for each corner, using the following pieces
|Brick 2x2 (3003)
|Plate 2x2 (3022)
Create four of these
and add one to each corner of the ‘floating’ base