Ok so think of the '3 c's' - close the reins, close the seat and close the legs. The seat is your most important and influential aid, so by 'closing' your seat, feel that you body has stopped moving with the horse, so that your whole body just says 'stop'. Most horses if they haven't been taught to run through a rein, will stop from this aid, or at least slow. The close of the legs, asks the hind legs to keep coming through, as a downwards transition is still a forward movement requiring the horse to remain engaged. The close of the hands slows the horse's forehand and is a 'backup' aid if your seat does not work.
I would say your horse is either nose diving onto the forehand through the transition, or becoming unbalanced and tense thus the head toss.
I would be working on a million transitions between all gaits, not just trot - walk. The more balanced through transitions he becomes (and this is through a building of muscle in the hind quarters allowing him to lower in the transition rather than nose dive or head toss to balance, and careful riding on your part - so don't lean forward into the transition, don't look down, etc. You want to keep as much weight over the hind quarters as you can, always thinking 'up'), the smoother the transitions will be.
I try to make some kind of transition every 10-12 strides, whether within or between gaits. Frequent transitions will eventually mean that the horse has to sit on it's hind legs to balance, or it will trip over! If you're doing trot - walk transitions, ride one transition to walk, walk for max 3 strides, the trot again for 10 strides, back to walk, 3 strides, trot 10 strides etc. And do this in various schooling figures like figure of 8's, serpentines, loops etc. You don't just have to stick on the wall or a 20 m circle. The more you mix it up the better your result will be.