This definitely got me over the hump. For a novice like myself the doc was not completely clear so I've given my final solution below possibly to help others. Notes:
1. The gui was created using app designer
2. I had to make the uiwait() parameter the giuFigure handle not the button handle.
3. Added the uiresume() with the parameter being the guiFigure handle used in the uiwait() of the .m program.
MatLab.m relevant code:
guiHandle = mySystemConfigGui;
guiFigureHandle = guiHandle.myConfigurationUIFigure;
gui RunPushButtonPushed callback
function RunButtonPushed(app, event)