I didn't examine the diagram in depth, but your requirements and questions suggest a "quick-and-dirty data acquisition vi" will not adequately meet your needs. Personally I'd refactor into a event-based producer/consumer design. Labview includes a "Producer/Consumer Design Pattern (Events)" template that is a good starting point. (File -> New... -> From Template -> Frameworks -> Design Patterns)
The template's consumer loop is set up as a simple message handler. At first glance it sounds like a state machine in the consumer loop will fit your needs better. I posted an example of how to implement a simple event based state machine here. Skip the Entry, Exit, or Transition actions if your state machine doesn't need them.
I strongly suggest sitting down with paper and pencil and creating state diagram that defines the core behavior you're looking for. It should include:
States: Uninitialized, Standby, Acquiring, Exit, Error, etc. These five states are probably sufficient for this app. Add new states if needed.
Transitions: Decide which transitions are valid and draw an arrow connecting the states. For example, it doesn't make sense to transition from the Uninitialized state directly to the Acquiring state.
Triggers: Triggers are actions that cause a state transition. List the triggers next to the transitions.
Guard Conditions: These are conditions that much be true for a transition to take place. Guard conditions are contained in square brackets following the trigger.
Getting the state diagram right will go a long ways towards simplifying the coding part of your application. Here's a quick example state diagram based on your requirements.