I will try to answer about the contour analysis and the lines between them.
If you need to turn the interconnected boxes into separate objects, that can be achieved easily enough:
- close the gaps in the box edges with morphological closing
- perform connected components labeling and look for compact objects (e.g. objects whose area is close to the area of their bounding box)
You will get the insides of the boxes. These can be elliptical or rectangular or any shape you may find in common diagrams, the contour analysis can tell you which. A problem may arise for enclosed background areas (e.g. the space between the ABC links in your example diagram). You might eliminate these on the criterion that their bounding box overlaps with multiple other objects' bounding boxes.
Now find line segments with HoughLinesP. If a segment finishes or starts within a certain distance of the edge of one of the objects, you can assume it is connected to that object.
As an added touch you could try to detect arrow ends on either side by checking the width profile of the line segments in a neighbourhood of their endpoints.
It is an interesting problem, I will try to remember it and give it to my students to grit their teeth on.