I don't think you should have lowered the rear in the first place. My daughter is less than 5'4" tall and manages my stock Ninja. She has a little trouble backing up if the pavement isn't level, but prefers putting up with inconveniences like that and not flat-footing to losing cornering clearance or suspension travel, or changing the excellent handling.
If you must have it lower than stock, lowering the front and rear 2" is preferable to lowing the rear 4" alone. That's still a lot, and may create problems like the front fender hitting something, you'd have to make some measurements to be sure.
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