How to isolate the wait function to one part of the code

I'm buildling an ecg montoring system along with programming an external stimulator using TTL pulses to work along side the information obtained from the ECG.The most important of  these features is the heart rate. However, whenever I activate my pulse trains in the code, the DAQmx Wait Until Done.vi function pauses everything in the code, including the part of my code that monitors the heart rate, which uses time to measure it. What I would like, is the wait function to only affect the pulse train generators without pausing anything else in the code. Is this possible? And if so how can I make it happen?
I will attach my vi
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simulatejed.vi ‏130 KB

Your problem is that everything is in the same loop.  So the longest operation is going to determine the loop rate (and therefore processing rate).  What you really need to do is separate your tasks into separate loops.  Use queues and/or notifiers to communicate your data and commands between loops.
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