Sorry guys, I am a complete moron. I said rack when I actually meant TOWER hence the drilling comment.

Good news is the tower went on without a problem and everthing lined up pretty much straight. Basically centered the the top point of the rear tower mounts with the last screw on the windshield mount. moved it a half inch up from the rub rail and started drilling. 4.5 hours later fully installed. The only problem I ran into was up front on the starboard side the interior glass of the boat goes in two directions, straight ahead for the outside lines, and curved in for the inside shell. This made for some pretty poor mounting locations for the backing plates.
Pic was taken in Bellingham out Bellwether Lane looking into the bay.