I had the same problem until I installed a solid rear motor mount. No more missed shifts.
Already have the mount, still have the issue although it's MUCH less prominent than it used to be. Might try one of them fancy torque dampers them ricer kids use.
It's worth trying Corksport's shift plate, too. I always through my throw was short enough until I drove Tom's car. The shifts were not only shorter, but felt much more "positive," too.