Thanks for all the info about the headers and the power jack. I never really gave the headers a second thought, until now.
I think I might go for the least elegant solution to this problem. I don't need the part of the proto shield that sits on top of the Due's power jack, so I'm probably just going to remove it. That part of the proto shield is for the extra push button.
Wanted to buy a nibbler a few days ago but couldn't justify it, due to lack of need. Now I need one and have to get one. That's a win!
Holger