I would recommend fitting the larger box in there since it will give you more room to manuever the battery and using the Optima battery so that even if you turn it upside down the thing won't spill fluid.
Suggestion though. If you intend to put the bumpsteer shims in the front rack do it before you do the box and change the bolts to allen socket heads. You will understand why when you fit the box in and see how close everything is.
Also, I'd recommend the banjo bolt, fitting and flexible hose line while you are at it.
Have fun mate! (no one noticed that my pedal plate is spaced out 2" for more leg room...)
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