I would highly recommend rebuilding whatever replacement shock you choose. It's the only way that you'll have one that is properly valved for your weight. Showa shocks for GSXR's incorporate a Schrader valve instead of the KYB's that require a needle to recharge, which makes them more friendly to self-rebuilders.
I would suggest that your choice be based primarily on length. A little longer is okay, but an extreme difference is a bad idea, and shorter shocks should be totally avoided. Weight bias shifts and trail measurements are critical to handling performance, so care should be taken to not engineer a death-trap. Forks can be dropped in the triples to maintain proper trail numbers, but fork length is often one limiting factor as to how long a shock can be safely used.
Also, swingarm angle changes with different length shocks and jockying fork height, and there are acceptability limits to that as well. A couple degrees higher is okay, but big increases are not a good idea, nor are changes that decrease the angle below factory spec.
Take lots of measurments BEFORE you start making any changes to your bike's geometry! You might be very sorry if you don't. Crashing SUCKS!! Swingarm angle, chassis attitude, and trail numbers are the three most important figures to pay attention to. After that the sag numbers are what you'll need to get right, but that's mostly a matter of proper springing.
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