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Create one checkbox for every pair. Put those pairs in the correct order in your form (given that HTML favours a left-to-right, then down layout), and display it appropriately in your template.
To create the checkboxes: Your form has a collection of its fields called fields, which is a dict mapping field name to field object. You will want to populate this programmatically. If you crack open the forms code in django/examine a form object in the shell, you will see (unless my memory is mistaken) that there is also a list or tuple of fields, which controls the order of iteration. You will want to populate this in the right order, as described above.
To display it: Iterate over the form in your template. You will want to include some information in the form, or otherwise pass to the template, to described the shape of the grid, so your template code can figure out where to put row boundaries.