Me. I'd check the tool change position box, set a safe position, and run (at a positively safe distance) it to see if that was all it needed.
Try just posting the output with the changes, and having a look to see the difference.
I'm getting to know my way around Gibbs a bit better, and my main bugaboo is that the process dialog boxes insist on remembering details from the 'last' job. <sigh> Getting used to checking those carefully!
Can't help you with the alignment possibles. I'd be measuring, not guessing.