Like many 3rd gens, my rear hatch is out of alignment. For some reason it does not want to lower completely to be flush with the rear quarters. I have already adjusted the hatch motor assembly to its lowest setting but it still is too high. I also adjusted the rear metal piece that connects to the glass to no avail. Is there anything else I can adjust that would possibly affect the height of the rear hatch?

 

The hinges. Moving them forward towards the front of the car will lower the bottom (spoiler part) of the hatch. Worked on mine.

 

Cool, I'll try that. Do you mean where the hinges attach to the body or where the glass attaches to the hinges? Also, It seems that I could adjust the pitch of the rear metal piece by placing washers between the glass and the metal on the four front most screws. Do you think this would work without making it look stupid?

 

Where the hinges attach to the body. There should be enough gap in the holes to slide it forward, and make the back end come down correctly.

That will probably make it look kind of odd. Plus, it would make a gap for water to run down into, and then rotting/rusting out your spoiler. Water might also run through the holes into the car too with spacers. Either that, or you will need a lot of sealant to close the gap and get a good seal. It still might look odd though.