@Rothrock I've updated the post to include an example of what the URLs are doing when I click on an item on the category page (seeing the blank Catalog-Item Reuse page and how I can see the details if I manually modify the URL without the appended Item-Category. Trying what you stated shows the url properly myUrl/1 but is page not found.

No, they are still the other way, would I need to do a full crawl for it to take effect? The URL that results is: myUrl/Pages/PageNotFoundError.aspx?requestUrl=myUrl/1/EDR1Ed‌​ucational%20Resource‌​s Now even removing what's in bold that gave me the item details is also a page not found.

If I use the manual option and set the url as myUrl/[ProductCatalogGroupNumberOWSTEXT]/[ProductCatalogItem‌​NumberOWSTEXT] I am then presented with Page not found instead of a blank page. If I edit the category page myUrl/educational-resources and view the query for the web part I notice that in the result preview it is showing the URLs as incorrect with the item category appended to the end. I'll place the screenshot in the main body of my question, so I thought it was something to do with the way search was indexing my catalog?

Hi @Rothrock looking at the catalog source settings it has, as I would expect, the column that categorizes items for navigation as owstaxidProductCatalogItemCategory (cannot change), Make URLs relative to this site selected, and Contruct a URL format from catalog properties selected with the selected fields being, from top to bottom, ProductCatalogGroupNumberOWSTEXT, ProductCatalogItemNumberOWSTEXT. This makes the URL underneath appear as myurl/Term Root/Term/[ProductCatalogGroupNumberOWSTEXT]/[ProductCatalog‌​ItemNumberOWSTEXT]. No mention of category after the ItemNumber property in URL.