First, you are starting the acquisition for each instance (loop iteration), this is not necessary.
Second, you need to set the acquisition to continuous, and the scan clock source to external connector. These are set at the AI Start. You don't need the low level start and control VIs.
Here is what you should do:
Configure your acquistion: Use AI Config Mid Level function. This sets the buffer size. The buffer should reflect how often you want to read. If you want to read and average 1000 points at a time, you just set your buffer to continuous.
Start the acquisition: This comences the acquisition of the data from the laser. You should configure this to read 1000 points at a time, or, alternatively, use DAQ Occurrences to read when the buffer reaches 1000. I used this method for a strip chart recorder to read buffered data and process it when it was available. This is a more advanced method, and I don't recommend using it right away. For now, just set the number of scans to read at 1000. Here is where configure the trigger. For your case, just set the scan clock source to "external connector". This is the PFI pins.
Read the data in the for loop with the number of iterations set to the number of sets of averages you want to perform. If this is done only once (i.e., you ONLY acquire 1 set of 1000 points, period, then don't use a for loop. Use the AI Read mid level function to perform the read. Set the number to read to 1000. This will read your 1000 points from the DMA memory location to your program.
Average the data. This is also done in the for loop, using the single function (Add array elements) after you have gleaned the 1-D array of data from your channel using the "Delete from Array" function. You will receive a single data point for each set of 1000.
After the loop, you need to stop your acquisition and clear the setup on the DAQ card. Use the mid level AI Clear function to accomplish this.
It is important to know exactly how the DAQ functions work, at least on a high level. I would suggest that you take some NI courses on Data Acquisition. There are books out there too, but the courses are comprehensive, and well worth the investment. Contact NI or your sales rep to find out about the courses.