Redfish, the balance of engine weight isn't something you can control so don't worry about it. Instead make sure you support the drive shaft so that it's not sagging and giving you a false reading. If it's a relatively short drive shaft then it may not be an issue, but I'd check to see how much vertical play there is in the shaft prior to performing the alignment and support it accordingly. The tolerances betwen the two plates are usually in the .004" range with a +/- of .001". (check your manual for the exact specs for your engine/boat) If the drive shaft is sagging it won't have to be so by much to throw your adjustment off. Also make sure the edges of two plates are aligned all the way around. You don't want any side to side offset between them. Good luck.