I have gone all through the controller and looked at most everything I can test to see if it might be the voltage firing the transistor to the outside world. Everything is surface, many have no markings that are usuble for identification. What appears to be the outputs are 6 pin parts, 3 on a side, 24 lives on pin 1 on all of them. The volatages inside this thing are not what I have seen, they change from 0, 2.6, to 5 on most parts when you change positions on the motor. That is above my head. I did manage to successfully get one unit to turn on and off an NPN transistor going straight into the base, 5V on the collector and 5/0 logic on the emitter, so that unit is reliable up to this point, the other only fires the .5V on certain position moves, not all, which leads me to believe that the position finish output is really a cumulative output of a number of other outputs in the box. I will be ordering one controller only for now it seems, better than 2!
The manual does not mention using a pullup, and they actually use only a 2k resistor and led for their demonstration units. I was using a 4.7k into a photocoupler to create some 5v logic, still unsure how I smoked it, unless without seeing it I dragged 24 across a trace.
Thanks for the suggestions.