I am having problems when I try to select a JGoLink that is at an angle. When I select the JGoLink, I see a rectangle being drawn around the JGoLink instead of just highlighting the JGoLink line. Any advice is greatly appreciated.
I guess you have made your JGoLink not Resizable, which is why you are getting a bounding selection handle rather than a bunch of resize selection handles at some of the points of the stroke.
You can call JGoStroke.setHighlight to specify a wide JGoPen of the color you would like. The highlight pen is drawn before (i.e. just behind) the pen of the stroke itself.
So in an override of JGoObject.gainedSelection you can call setHighlight, and in an override of lostSelection you can remove the highlight pen. The FlowLink example class in the Processor sample application demonstrates this. Note how it also avoids recording the change in the undo manager, since presumably the highlight pen is not really supposed to be part of the state of the document.