@Tim Franklin I don't have a ton of experience with UoM in NetSuite, but maybe I can help out on the Celigo end.
So you have some of your items setup as item groups, and some components within the item group have differrent UoM, right? For example, you have component A with eaches and for component B you have a UoM of case and that case includes 2 eaches?
When sending the fulfillment information back to Shopify, what do they expect? Do they know what makes up the item group or they only see it as a singular item?