Use the Schedule Library and the related Copy Commands from.
Divide the long schedule into multiple sections and string together multiple Copy Commands from..., remembering to choose Library from the list, together with wait commands. It's recommended that you put in a Wait... with about 20 seconds in between each of the Copy Commands driver commands. You may want to put in longer, but 20 seconds is the recommended value and seems about right as this gives the commands a chance to load up, and looks realistic as the locomotive stops and waits as if the driver is waiting new orders.
Splitting up the commands in smaller batches makes troubleshooting a whole lot easier as well and also makes modifying the schedule or schedules a lot easier. If you have multiple locomotives performing similar things, you can modify different parts of the schedule to suit.