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No, The Big Sucker Stage II is just a stage 1 AC with a slightly larger air filter. They just call it that to differentiate between the two. Use which ever one you want. I put a stage II on my Sportster.
Ditto what GhostRider58 stated. The Stage I is smaller and can be used with your stock football cover and the Stage II is larger and requires a cover other than the stock football.