After determining that the RA motor was not returning positional readings from the encoder, we needed to test this to see what we could do to repair it.
Replacement motors are difficult to come by, and potentially need to replace the entire RA assembly (cost is about AUD$500). The encoders that are made by US Digital are no longer available, and their "drop in replacements" are not actually available in the correct bore diameter.
We wanted to prove the problem was with the encoder itself, not the motor board, to determine what parts needed to be repaired.
With the purchase of a $20 logic analyser off Amazon (https://www.amazon.com.au/gp/product/..., we were able to determine that the encoder was at fault.
Luckily, the guys out at Bintel (http://www.bintel.com.au) were able to ship me just the replacement motor at a decent price, so we were able to fit this and test the result.