Does anybody prefer the standard suspension geometry over what seems to be the norm of raising the forks through the yokes by 7-10mm?
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As a fellow FZS 600 owner (2000 model-2001 Reg) the single best improvement I have made to my 15 year old machine was to replace the rear shock with a Wilbers unit & have the front forks rebuilt with new springs,seals,& heavier weight fork oil.
Before you ask about "standard geometry" check that your bike is handling as it should be considering its age. Ultimate handling will depend on various factors like suspension condition & function, swingarm ,suspension linkage & wheel bearings condition, and tyres(condition,wear, type, pressures).
Once you have the best "standard" set up achievable you can then experiment with adjustments-eg sag etc, taking your "all up weight" into consideration & making changes to dog legs(linkage pieces), raising/lowering forks through yokes to achieve best results for your personal preferences.