Hans,
Unfortunately I wasn't able to open your VI but I will give you my suggestion anyway.
As you probably have noticed, the counters are not capable of generating that long pulses, so that leaves you with the options of digital or analog output.
The digital I/O on the E series devices doesn't support any handshaking, so you would have to generate a DAQ event from your trigger and then write to the port.
You can trigger the analog output operation with a digital pulse and reset the output value when your timer loop reaches a certain value. You don't necessarily need to use a local variable to pass this information out of the loop (assuming you want to keep the loop iterating). The LabVIEW occurrence is a nice way to implement it (under Advanced -> Synch
ronization palette).
It's going to take almost 25 days for your iteration terminal to roll over at 1 ms iteration. When it does the output from the terminal stays at the maximum value, 2147483647. If this is a problem you can check for the terminal value and when you reach start counting the following iterations using a shift register.
Kai