Problem #1
Bob can decrypt the message by splitting the encrypted text into a 3x3 matrix, then multiplying the encrypted by the inverse of the secret message matrix. The secret message is also a 3x3 matrix.
Problem #2
No she cannot figure out the secret message without finding the inverse of the secret matrix. As of right now, I cannot think of another way to decrypt the message without using the inverse of the matrix.
Problem #3
Step by Step equations to finding the ecrypted message:
$ \begin{bmatrix} a & b & c \\ d & e & f \\ g & h & i \end{bmatrix} x \begin{bmatrix} 1 & 0 & 4 \\ 0 & 1 & 0 \\ 1 & 0 & 1 \end{bmatrix} = \begin{bmatrix} 2 & 0 & 0 \\ 0 & 1 & 0 \\ 0 & 0 & 3 \end{bmatrix} $
