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I've build this in stages, the first stage across the top uses the MB Affinity tool, which determines the number of basket associations between codes.
I then built a macro which loops through each Stock Code and transaction number and creates an association using the append tool between all combinations. This allows me then aggregate up to each unique combination (or at least unique in terms of primary and secondary code as per your required output).
I then joined the two phases together and created the desired output.
unfortunately, what you're trying to do requires all combinations to be identified.
I've attached the original workflow with the macro zipped. This should create only the combinations per transaction number, which means it will only create the combinations that you need.
With a large dataset this will take some time to run as you are literally trying to create every possible combination in the set, there's not really a way around this as it's what you're trying to achieve.