The speedometer drive runs off a worm gear at the transmission output. I know nothing of the Miata transmissions, but it seems that their worm gear may have a slightly different ratio. I'm surprised that the people who sell the conversion kit haven't done something about that.
Before doing anything to compensate, you need to know precisely what the difference is. That is best done with the odometer. Be sure your tire pressures are right, then see what your odometer indicates over a several mile stretch of road; mile markers on the freeway are perfect for this. Once you know the error exactly, you can shop for a correction gear such as the one John identified.