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With a 54mm on a stock 749 you may notice a little loss on the bottom end, say up to 5000 rpms. This can be helped with a custom mapped FIM chip or power commander. Take it to a dyno for a tune. The 50mm will work well all through the powerband. Something to consider, do you forsee engine work down the road, Hotter cams, bigger valves or even a big bore kit? If you may plan for this later, buy the 54mm now. That way down the road you wont have to replace a pricey exhaust system just to upgrade 4mm's to accomidate new engine mods.
My 2 cents...
My 2 cents...