430 How do I adjust then tonneau cover properly on my spider?

Have you checked to see if the two allen bolts at the base of the capote cover are loose or mis-aligned? If you slide the cover back towards the rear of the car (interrupting the opening process before the cover starts to go vertical), then check at the joint were it pivots at the rear, you'll see the capote cover is attached using two hex screws per side. That is also for alignment. It looks like your cover is shifted toward the driver's side. I'd carefully try to align it using those to get it straight and see if it improves. That may cause the tooth to catch accurately, drawing the front lower and out of the way of the top mechanism that scratched it.

 

In the very first picture it could be possible that the pin is bent. if the pin is bent up, it could make your cover lower as it's coming in to close. so check what eric above says to make sure those screws in the back (under the cover) are tight and didn't come loose. And also check those pins to make sure those bolts are tight and that the pins did not get caught up and bent

 

the two guide rods need to nicely slide in between that plastic channel guide without touching the sides. its its rubbing its actually then flexing the tonneau cover. Let the tonneau cover go down after you loosen 8mm screws and see where they need to be in proper position then snug them down.

 

FYI I know i said pins, but guide rods is a more proper terminology