I also still having this problem. The only lyrics solution I've come up with, at this point, is to try and meeting at the first intersect point (which requires more fuel, because of the extra speed) or "guess" on the separation for the second intersect and then adjust at the apoapsis. After you setup your initial maneuver, warp to the apoapsis. The second intersect point and separation will then show. Usually, I can turn prograde (orbit relative) at the apoapsis and use my RCS to burn a little faster or slower and get the separation to a reasonable distance.