Your logic for the booleans looks much better. Though the start of your acquisition relative to your digital pulses is unknown, as this is all timed in software. Once you switch to an M-series it will be very easy for both of these tasks to share a trigger. You won't be able to run them on the 6008, but you can look at the examples under DAQmx>>Synchronization>>Multi-function.
Great, it is the perfect time to upgrade for you. It is always good to see people growing in their skill as DAQ programmers and pushing on to the next level of hardware. The M-series will really give you the flexibility you need.