I haven't had much experience with trotters but my friends that do all seem to say check for soundess issues, as many gaiting issues with trotters is due to that. You're on the right track with looking at the shoeing as well. A very good vet told me a lot of trotters when they skip to a pace is it mainly due to soundess issues.

If you can get your hands on some McTarnahans Blue Lotion, mix 2 parts blue lotion to 1 part water. Then rub onto the horse's lumbar region, sacro-illiac (sp?) junction, stifles and shoulders. I've had horses a bit sketchy seem to get a lot smoother in their gait by doing this every day. One horse I had, a pacer, was putting in some hops while at speed, the blue lotion routine coupled with 3 months depomedrol (sp?) injections into the site on his rump that bothered him (diagnosed by a vet) and he was as good as gold

I'm sorry it's not much help - it's very hard when you can't see what is happening/drive the horse yourself. Good luck