I followed the body line below the side windows. You can see the body line I used on this pic of Kevin's truck.

I used 1/8" steel plate welded across the tops of each side and the rear door. Both hinges are at the bottom half of the rear door, so there's nothing to do.
Where I cut it does make the elevation of my front doors a little bit higher than the tops of the "bedsides",

but I needed that space to attach a hard top to. I also thought it would look funny to have that body line so close to the break-over. I intend to make some nice rails that will bolt into the inserts for the hardtop that will make the front/rear elevations match. And/Or... I may pick up another pair of doors and make some half doors.