Sliding up into the dodger meant that water could not run down the dodger and catch on the top of the glass and then find a way to dribble down the inside of the windscreen. The same thought process went into the port side operable windscreen.
Good luck with your replacement! I would definitely go with the reinforced Sailrite type pattern material. That way you can mark where the current screws are located and have them drilled out.
Other folks have taken care to paint the part of the windscreen against the dodger grey or black to prevent the caulk from showing through, or some ugly mold etc.