With the rear skirt sikaflexed in place, I could now clean out the holes.

This is more difficult than it sounds. The sikaflex is all rubbery and hard to remove and I had to get a clean hole access again to the pop rivets to connect the canopy to the frame.

With a lot of patience and spending way too much time, I finally could get back to the countersunk holes in the canopy bubble. 

Pulled out the hand rivetting tool and pulled the remaining pop rivets so that now the canopy is fully attached in the rear to the canopy frame.

Finally I mixed up some micro and filled the holes which you can see in the image.