you should probably add self-study tag to your question. you are using a scholastic dataset, aren't you?

I'm sorry I don't understand what are you trying to say with: "I can simply take the unique list of products between the 3 and then fill the space in the stores with the products where the products are ranked based on £/space"

that could be, in fact I made some confusion and at first I wrote the code with products on the rows and stores on the columns, but I fixed it before you posted this comment and it should work, grouping stores. dist(dt) takes rows to be the units to create distance between of.