I reran the process. After rezeroing the axes (again). And had the speed slider set to 5% of the programmed speed. And spend the entire 25 minute process with my hand held against the eStop. And twitched at every noise.
And it ran almost absolutely as planned
And, whilst I haven't checked it's exactly dimensionally accurate still (if it was to begin with) it seems pretty good.
So whilst I'm not certain what went wrong at least I have a little confidence back.
My coworker very helpfully told me "Well you need to work out what went wrong so it doesn't happen again". Well yes, yes I do. But I've had one ten minute tutorial on this machine and everything else has been Google and Youtube so how exactly do you expect me to divine the solution?!
I kind of don't want to learn too much of this because it's something he "can't be bothered to look after" and hterefore want's to slope off onto me but it's something I want to learn for my own skillset.
Anyway. I'm off now till Monday and I will pick up again then.