If it's not too late, a good test to find if water is still entering is the tape a piece of plastic wrap or other clear plastic over suspect areas. Tape the entire perimeter. After a rain, check the plastic. No droplets? Yay! (Also wait a day for soaking through time and re-check.)
It also may help to install a rain cap on the chimney if it's got sectional flue liners inside. Water gets through the joints in the liner sections, wraps around the edges and goes to the bricks.
Best of luck with this challenging project. It sounds like you're on the way to success!
Paul