After getting the quarters pretty clos to level with the decklid, I started checking the gaps and found nothing would line up. I then squared the decklid with the car with lots of careful measuring and tightened it down as a gide for the rest of the work.
I started with the passenger side and just cut a slit from front to back and used a straight edge and screwdriver to work it into a decent gap. I'll have to work it some more once the gutters are in, but I'm now at a good starting point here.