yea, my hatch was pretty bad too. Did the same thing, adjust the doors until your bead lines up at the front where the fender is, then in the rear towards the quarter panel. You can take your striker off (the inside wall of the door jam, NOT on the door) To make it easy to open/close. Then put your striker on, and adjust it where you need it to be.
I found out my striker was pulled out, so my door would never shut tight enough to close the window gap, once I pulled it in, it was fine.