Did some more trials and testing today, but first I will answer the questions.
The 3/8″ is the difference in the y axis gantry rail to outer rail end to end (see attached picture in previous post). (i.e. one end has the gantry and outer rail 4″ apart, the other end is 4-3/8″ apart) The Diagonal measurement to the corner blocks is within 1/16″.
Trials today. I was able to get the starting distance between the gantry rails and the frame rails parallel to each other. Power on the controller and re-checked the distance and it was still good. I jogged the gantry almost the full length of the x axis and back again. On the extend motion The y gantry y rails ended off about 1/8″. On the return motion they ended up being 1/4″ to 3/8″ off. It was always the same, the gap got greater on the end away from home position. I then drew a rectangle and noticed that x side away from home measured shorter. It looks like the return move was shorter than the outgoing move. I have tried to capture this pictorially with the attachments.
I also noticed that when I power of the controller the steppers are not energized to hold position. After a move they are energized for a time and then seem to “relax”. Does this sound correct.
Any thoughts would be welcome.