If you're going to be bombing about at high speed, you will want to give yourself some added up travel - probably have your shock sitting around 7 inches of extension (leaving you 3") to soak up big hits at high speed without bottoming and taking control away from you.
If you're going to crawl you probably want to give yourself a bit more down travel, and sit at something like 3-4" of extension (6-7 inches of "droop") - the limited compression won't cause major problems on the road or at moderate speeds off road.
Going straight in the middle is a compromise - it's functional without giving emphasis to any one thing. As was alluded to, the first thing is to make sure you have the proper bump stops to keep your shocks from bottoming out if using a shock with a longer collapsed length than stock. You'll find that you need shocks and springs that work together to achieve this synthesis intentionally. Otherwise, you'll end up wherever you end up up because your lift is built around the "height" or the springs rather than your shocks and articulation...ask me how I know this.
OK, since you asked - I did my lift around the springs. Now I'm waiting to pick-up my second set of springs and waiting for an opportunity to upgrade my shocks - primarily because I want to optimize my shock travel. If I'd built my lift around the shocks in the first place, I'd be better off.
Standard procedure for setting the suspension on a dirt bike is to reserve 2/3 of the suspension travel for compression, leaving the remaining third for extension.
From Sway-a-way.com "Ride Height is the height of the vehicle standing still on level ground. Ride height for high speed desert applications usually vary from 30% to 50%. Ride height for slow speed rock crawler applications usually vary from 50% to 70%." In this instance, ride height can be considered equal to the extension side of the available wheel travel.
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