When I join a rally, the system will not let me enter ALL my elite guard troops. How do I fix this?

The reason for this is your march size. There is a limited amount of troops you can send at one time. That's why you have separate march queues. The more you upgrade your town center, command center and embassy, the larger your march queue and reinforcement queue will be. You can find out how big your march size is by clicking somewhere to camp and looking on the bottom right side of your screen for the limit.