Why are your steps per so high with the g540?
A typical setup on a system using 5 tpi ballscrews is only 10,000 steps per in Mach's motor tuning.
200 (steps/rev) x 5 (tpi) x 10 (1/10th microstepping) = 10,000
your 3.6 motors would be half of that, 100 x 5 x 10 =5000
What microtepping are you trying to run on the 5056D?
What's your leadscrew tpi?
The LED on the 5056D isn't flashing is it? That means the supply voltage is over 45V.
The calibration wizard will help fine tune it once you're in the ballpark.
http://www.youtube.com/watch?v=XkO5tc-jSxw&feature=channel_video_title]Improved Mach 3 Axis Calibration - YouTube