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I have been working a little more on this and have a workflow that now seems to work - the output at the end was basically what I am looking for, but I'm not 100% happy with the method of getting there as it is quite ugly and also relies on the automatic renaming of duplicate columns.
The original Excel table has headers that I need to be able to reference for each data point, which was the reason for the dynamic rename...
@jdunkerley79 thanks i really like how you used record id here to split out the fields that needed sorting before bringing them back into the rest of the workflow, rather than reconfiguring the entire thing like I was trying to do.
I love Alteryx, but learning it is tough! Amazing the support in this community.