I do not have DAQmx or any suitable DAQ devices so I have not tested this.
This is a start on cleaning and speeding things up. Note that writing to the front panel indicators at 1 kHz will not work because the screen update rate is on the order of 50-100 Hz. Also charts take a considerable amount of computation beacuse they need to (1) store data in the internal buffer, (2) erase old data if the buffer is full, and (3) (slowest) recalculate all the pixels in the display for the updated data. The cart should be moved to the parallel loop. The condition True boolean will only be true for about 5 ms out of each 100. Look at the 5 ms boolean.vi attached. It runs close to 1 ms per iteration. The boolean is true about 5% of the time but I never see it change. Remove that boolean from your VI.
With continuous sampling on the pulse channel and reading 1 sample every millisecond (assuming you get that fast) when the high speed sampling occurs it takes 5.4 ms to acquire the 270 high speed samples. So, ten times per second the loop takes >= 6.4 ms for an iteration. The next sample it reads from the pulse channel is the one which was measured (acquired) at 1 ms after the previous sample. Thus, this data point is read ~5.4 ms after it actually occurred. The next time you detect a pulse, it will be 5.4 ms late. The second one will be 10.8 ms late. Eventually you will get a buffer overflow, but your data will be useless long before the error occurs.
The Dual Sampler Simulator.vi shows a possible approach to the issue. It simulates sampling both channels at high speed. I generate both a sine wave and a square wave and sample both at 50 kHz. It simulates reading 4000 samples at a time (equivalent to reading 12.5 times per second or every 80 ms). The square samples are then processed for the transition using the boolean Implies function. I do not recall whether the Conditional terminal was available in LV2012. I did not get an error when saving for previous version so I think it will be OK. The same thing can be done with a while loop with some extra logic. This does not handle the case where the transition occurs at the boundaries of the 4000 sample segment. To handle those cases use a shift register on the outer loop to pass the needed samples to the next iteration. The 800 ms Wait makes it run slower than "real" time but allows you to see what is happening.
Lynn