Have you tried alternatives to Y raises? Like theraband pulldowns (theraband over a door or high pulley) in sitting, or activation in sidelying? It might be that you are not strong enough/don't have enough activation to complete the Y exercise properly yet. Start of with the easier exercises and make sure you can do them really well (i.e. good activation of lower traps and no upper shoulder tension) before progressing. You might even start in supine and feel the movement of your scapula against the bed.

Your difficulty in using your lower traps is likely to be related to your whole body patterns of movements and postures so pay attention to these throughout the day. Make sure your scapula are well placed before moving your arm to reach for something, for example. Also be aware of avoiding a forward head position/posture and rounded shoulders as this will increase the resting tone of upper trapezius and levator scapulae and make them easier to activate and use than the lower traps.