Then take the bumpstops off, then see if the shock bottoms out. If not, then don't worry about it, and put the bumpstops back on. After all the rubber bumpstops squish down somewhat.

Depends on how you lower the rear. Flater leaf spring, adjustable/different spring perches, or spacer blocks between the spring and axle tube - which doesn't effect the shock length as the shock plate will be in the same location relavent to the upper frame/shock mount.

And you also have to allow for any additional movement that the rubber bushings in the lower control arm to frame mount, IF they are rubber. Even poly will have a slight movement under extreme pressure of hard cornering and dips and bumps at speed.