Well, first off I'd tell her to stop lunging him for so long - not only is it possibly doing damage to his joints/muscles etc, but its only going to make him fitter!!!
My coach suggested that before I even hop on my OTTB (who is very VERY sensitive and also can have high engery moments) is to do ground work with her on a long lead rope. I.e. Walk her forwards a few steps, then get her to stop, then back up a few steps, then do it all over again. Then when she is calm with that I add in asking her to step sideways/forwards a few steps etc etc. Only when she is calm and relaxed looking, do I then get on. If she jigs/walks forward when I try to get on, I start all over again!!!
THEN when I am finally in the saddle, I WALK until she is walking with a relaxed and calm manner and walking a clear 4 beat walk. My first lesson with my coach, we walked for the WHOLE 45 mins! And it was the best thing for her! After that initial lesson, the amount of walking we needed to do deminished greatly. Now when I ride her, I might need to walk her for 5 mins one day, 15 mins the next etc, but I do it all with my body sending out the RELAXED signals.
Then when I do trot, again - its all about being relaxed....
I know it sound tedious and slow, but trust my, my mare has come along in leaps and bounds. After 10 rides riding in this manner, she is walking and trotting in a (mostly) relaxed manner, and her paces are even and regular! Plus she is more likely to pay attention to me!