That is the right transducer. It is a transom mount, Mega SI for Helix, with temperature. You are correct in that the other side of the Y cable (pigtail) is for the glassed in 2d transducer. Leave it as is. After you have fished the new cable from the transom to the dash, simply unplug the old SI connector from the Y cable, plug the new one in, and then re-connect the Y cable to the back of the head unit.
It is probably best to leave the old SI cable as is, rather than trying to pull it from the console to the back. It likely is tightly bound in the conduit, and, if trying to pull it through, may get jammed, and/or upset other wiring. Cut the cable somewhere in the rigging area, and simply remove the old transducer.