You are correct, there has been a bit of a paradigm switch from traditional to mx for counters. The information Ames provided will covers many of the differences.
One thing I noticed from your description is that it sounds like you're not actually wanting to get your pulse width measurements in time, but rather in ticks (as they would come in traditional daq).
I'm attaching a modified example that sets the GATE ("input terminal" in mx terms) and SOURCE ("counter timebase source" in mx terms) to RTSI0 and PFI39, respectively. Another thing you should note is that the "units" on the create channel VI is set to "ticks". If you measure in seconds, then you have to provide a rate for the source. From your description, it appeared that the rate you have conne
cted to the SOURCE is the unknown that you're measuring.
Hope this helps.
gus....