i have had three lowered s series one dropped 3/5, one 5/7, and one 2/3. ive never had a problem bad enough to have to get he ds shortened, but i have had pinion angle problems. i just consider myself lucky. if it doesnt cause a driving problem maybe next time put a jack under the tailshaft of the tranny and put a little tension on it to give u some more room to get the driveshaft out.
When lowering a s series u are ultimately relocating the position of the differential(rearend) under the truck. When this is done the distance from the yoke on the rearend and the output shaft of the transmission is shortened in length. You also change the pinion angle of the truck when lowering. MOST trucks can get "AWAY" with not having the driveshaft shortened or messing with pinion angle. I say this very loosely cause every truck is different. Even if they are both the same year, same drivetrain, and same model (std cab or extcab) they will have different characteristics.