Congratulations once again on winning Rookie All Star! You guys deserve it. I know you were disappointed by the hand you were dealt at North Bay but you took it all in stride and everyone was focused and got the job done. Robot issues aside, you impressed everyone with how well put together your team is.
As others have said, your priorities for defense are:
1 - don't let them near the batter (play Pong - drive back and forth across the defense line, blocking their way in). Make them waste time trying to dodge you.
2 - if they get past you, bump into them, disrupt their ability to drive to their preferred shooting position. You don't necessarily need to pin, just give them a good shove to knock them off and force them to realign over and over again.
3 - All the high goal shooters I've seen so far take a while to line up their shot. Generally they need to position themselves just right, then it takes a few seconds for some kind of aiming system to find its target, then spin up motors, then fire. Learn how long this takes. After slowing down access to their favourite spot, then forcing them to realign again and again, leave them alone for "not quite long enough", then give them a good bump just as their shooter fires. Make them waste a bunch of time only to miss the target when they finally are able to fire!
4 - If one robot has come in and already fired its shot, and is on its way back out, and another robot is inbound, don't bother continuing to block or bump the robot that's leaving. Let it go, and focus on the incoming one. Of course if it's just the one robot in the courtyard then feel free to block it, incoming and outgoing - slow it down as much as possible.
5 - train your human players to either get the boulders as close to the defense line as possible, for your offensive robots to have easy access, or to keep them inside your secret passage, where it is riskier for the opponent robot to waltz in and grab one. If they do go into your secret passage, go after them and bump them around. They will get a penalty for your contact! (Check with the ref before you do this, but according to the rules and the Q&A, this seems like a valid defense strategy)
6 - if they miss a shot, beat them to the ball, push it into your secret passage. Deny them the opportunity to grab it back and retry their shot.
7- as others have said, another way to play defense is to attach a nice tall opaque wall to your robot, not necessarily just to block/deflect flying balls but also to obscure the driver's vision of their own robot. Maybe a big version of your team standard with the word "Checkmate" clearly visible?
Best of luck and have fun at Worlds - hope to see you guys again!