My only concern is for your selection of motors vs the G540 controller. The G540 really does not like anything above 3 mh of inductance. With your combo your motors will be about half of there capacity, ie 425 oz really will be 212 oz. This might still work for the X&Y at a reduced speed but the Z axis at 300 oz might have some problems running without a counter weight or gas spring. For those choice of motors the g302's would have been a better choice with a higher voltage supply. If you really want the G540 I would recommend changing the motors to 381 oz from keiling and the 906 oz for the Z, both of these motors work well with the G540.
One other note on your homebrew supply, if you don't have large filter caps on the output you will need to add some, also after the caps are in place make another voltage reading of the power supply, the G540 won't like anything above 50VDC.
Let us know how it goes,