The short answer is I tried to short cut. The problem with that is it blinds you from what's right in front of you.
Very true. The steps per wizard is a perfect example of something that shouldn't even exist IMO. Folks that know what they are doing don't need it and folks that need it don't know enough to use it. But if they do it gives them a false sense of security (they assume their problem has to be something else). The only correct way to set steps per in motor tuning is to do the math (plain and simple, no 2 ways about it). There are too many other variables that can make one think the steps per are spot on when they could be off significantly. To add insult to injury any error in the steps per is cumulative. So, if you set you steps per incorrectly because you relied on a measurement that was flawed due to skipped steps, backlash, flex, etc. However much it is off in the distance used is multiplied by the times that distance will go into a move.
The best most of us have that is even capable of measuring close enough to do a good job checking steps per is a dial indicator with 1-2 inches of travel. Take the best indicator in the world and take measurements and adjust until you get the steps per perfect and you can still be way off if some of the related variables are not accounted for. Lets just say its off .010 in one inch of travel because backlash while measuring wasn't avoided. At 8 feet it would be off almost a complete inch (.980). Steps per can get out of hand real quick and the only right way to do it is doing the math.
Tons of material available to teach folks how to properly tune motors. Tons on this forum, in our docs and other places online. Anyone attempting to tune motors need to spend the time to understand what it is they are doing and how things not thought of can give false readings. There really is no shortcut to do it right. Sorry you learned this the hard way but glad you learned.