Hi there, if you still need, I explored changing the Separator color in a Side by Side question in this post a bit, but the code I posted doesn't change the color of the top portion of the Separator. To change the color of top portion as well, I used the id of the top portion element which can be found using the inspect browser tool. Like with the bottom portion of the Separator, the Separator color is driven by the "border-right" attribute of the first of 2 Separator elements that follow the column or table cell (Separator1 and Separator2). In your case, the id of the top portion of the Separator between columns 2 and 3 is "style~header~qid~4~2", like in the below screen shot. For the bottom portion, using the inspect browser tool and the approach described in the other post, the Separator between columns 2 and 3 is c12. So to change the color of the entire Separator between columns 2 and 3, try adding the below to the question's JavaScript in the OnReady section.
var qid = this.questionId;
var topsep = document.getElementById("style~header~"+qid+"~4~2");
var bottomsep = "#"+qid+" td.Separator1.BorderColor.c12";

jQuery(topsep).css({"border-right":"2px solid red"});
jQuery(bottomsep).css("border-right","2px solid red");