Thanks guys, I really appreciate all the help.
Rich, I downloaded and printed out the PDF file and it has really helped me to make sense of it all. It really is quite simple, but after thoroughly confusing myself messing around with so many things, I really need to stop and think about what I'm doing.
Part of my problem was not zeroing the machine, so things were getting out of wack combined with improper values, and in some cases I had the motors reversed only to add to the chaos.

Your directions should get me back on track.
Thanks!