Drawing such graphics is much easier if you simply work on a grid. I would draw those on a 1mm grid, which makes it very easy to line things up.
Also, if you drag one of the end points of an arc around, then you also change it’s radius.
I would not use [F] for flip. Flip is for moving stuff between the front and back side of the PCB. Even though lines (and arcs) on Edge.Cuts will stay on that layer, you still only get two orientations. Use [R] from Rotate instead.
As long as you snap the end points of the lines and arcs together, it will be a valid outline, even when the lines are not perfectly horizontal or vertical and there will be small differences in the radii of the arcs.
Malformed Courtyard
The Courtyard layer is for “reserving” space on the PCB for each footprint, so they can be placed with automated equipment. For this, the rules for the courtyard layer are very similar to Edge.Cuts. Very likely the person who made the footprint for the arduino PCB placed the connectors on it, and together with that the lines of the courtyard layer for those connectors, and those lines overlap. To fix it, load the footprint in the Footprint Editor, and change the lines on the couttyard layer so they do not overlap or intersect. Snap the endpoints of lines together, just like for the Edge.Cuts layer.