I found some issues. Firstly, your missing an underscore in the .rds file (Cape_York_Invasion...).
Second, you haven't enough waypoints between locations in both your .rds and .srd files. You need at least 8 waypoints for each route. For example, this one only has two:
[Cape_York_Invasion_Beach to Cape_York_Invasion_Beachhead] 87133.79 55235.73 120.00 0 2 2.6388890743255615 86471.82 56152.94 120.00
Finally, if you've modified the class and payload files, you'll also need to update the allpayloads file as well.
I'm not sure that's all the issues with your files, but those are the things I've noticed at a glance.