Pretty difficult, but still good. I'm going to include the solution to the semaphore puzzle as the other comments didn't explain it and it was really difficult to figure out.
****SPOILERS FOR PUZZLE****
You need to direct the light to each direction individually by clicking on the circular light symbol on the light activation thing. It spins when you turn it on, but if you turn it off, you can manually redirect the light. Each time you do, go back up to the observation deck and look out the window with the light, and take note of the position of the guy in the boat. Do this for each window/symbol, using the chart to convert the flag positions into the numbers.