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Sure you can. Post your code when you get it working, or a question otherwise. Good luck

You can omit the repeated lines of code. A pseudocode:
while(playersInputIsInvalid) {
System.out.println("We have no idea what you meant!");
getPlayerSelectionAgain;
}
if(playerSelectsThis) {...

I don't get what you mean by a "Challenge" generator.. but for multiple arrays:
Multi-dimensional arrays, like int[][][] for a nice 3D setup
ArrayList - a class made for toying with data

Eh,...