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This answer explains that the alignment of the joints varied slightly between each Canadarm on the Shuttle. The amount of correction for each arm was known and programmed into the flight computer.
The information loaded into the flight software was carefully checked for the real Orbiter and I am unaware of any issues caused by a serial number mismatch in flight.
Were there visual targets on the Shuttle to confirm the alignment?
Yes, whenever the crew was preparing to grapple a payload, they would fly the arm to a defined pre-grapple position. The checklist gives the joint angles expected at the position.
This example from the STS-127 PDRS checklist shows the joint angles and two camera views expected at the position. The end effector camera should be lined up with the grapple target on the payload if the joint angles are correct and the correct set of encoder biases is loaded into the flight software. Using DOUG visualization software we can see what the view of the grapple target through the end effector camera would look like. The green crosshairs on the crew monitor should line up with the crosshairs on the grapple target.
Visual alignment confirms that all is well.
Of course in the real world perfect alignment is not expected, the payload can shift slightly in its mountings due to tolerance stack-up or thermal effects.
Addendum: grapple overlays and grapple targets
A transparent grapple overlay was placed on one of the shuttle aft flight deck monitors when preparing to grapple something with the RMS. The overlay worked in conjunction with the end effector camera. Printed on the overlay were the correct camera settings.
(from the linked checklist)
Grapple fixtures had a 3-D grapple target on them which was used with the end effector camera / overlay system to align the arm for grapple.
(personal photo)
A description of how to interpret the errors, from PDRS training material:
Target Cues
General rule of thumb (although errors are usually coupled) is
Translation - primarily white dot in white circle
Rotation - primarily crosshair in black circle
White dot maintained within or on white circle
Cross-hairs are maintained within black circle after alignment
Visual envelope at tip of grapple pin corresponds to:
± 10 degrees roll
± 10 degrees pitch, yaw
± 2 inches in EE Y and Z
Allowable pitch, yaw errors change with distance from the pin
