In this situation there is no point using the configuration wizard + dial indicator method. All that will achieve is, at best, to make the distance moved more accurate between the points you've measured and also most likely reduce the precision over longer distances. Lets say you use a 10mm travel, 0.01mm resolution dial indicator to 'correct' the error. The indicator will measure to +-0.005mm (approximately), so over a distance of 300mm you've introduced an error of 0.005*300/10=+-0.15mm over that distance. That's far worse than the lead error on a standard C7 grade ballscrew which is 0.05mm in 300mm, and no doubt worse than your average lead-screw.

Even if you use a 300mm digital calliper to get +-0.005mm over 300mm (again approximate - look at the manufacturers tolerances for the calliper) all you've achieved is to find the distance between the two points in the screw you've measured - who knows what variations there are in the pitch between these points? So there's just no point... calculate the number using the method HiltonSteve suggested as that's the best you can expect to get without mapping the whole screw.