The little breakout relay board arrived today. It only took a short while to get it wired up. It worked on the first try. I have added some buttons to the screen to control the relays manually (even got an LED to turn on and off, which is very basic, I know, but it was pretty advanced for me). I then added some code to the macropump to turn off the power to the motors (not the controller board) and the laser power once the files have reached 96 (the end) and the probe has returned to the home position. It took me much longer to do the code because it was pretty much trial and error, but it works.
It all seems to function well. I may try to add some extra features now such as the option of running two or three plates at one time instead of just one. Overall the system seems to function quite well and is pretty robust so far. And now I have saved myself a lot of money because I won't have to replace the laser as soon
Thanks, y'all for your help on this.