Tente o seguinte:
SELECT c.original_SKU, c.bought_with, count(*) as times_bought_together
FROM (
SELECT a.sku as original_SKU, b.sku as bought_with
FROM items a
INNER join items b
ON a.order_id = b.order_id AND a.sku != b.sku) c
GROUP BY c.original_SKU, c.bought_with
