Hi John,
find attached a jpeg - picture from an init-sub.vi. There you can see, that this initialization phase consists of some sub.vi's who are in charge to init different equipment. The main thing is: an error-line is used to make sure the order of execution. You should do this in a similar way. Some init vi's are inside case-structures; these instruments are not in use for all of the measurements.
Hope this gives you an idea, how your problem might be solved.
regards
wha