Data acquisition with highly accurate GPS time stamping (hh:mm:ss:sss UT)

A research group has developed a data acquisition system dedicated to daily observations of solar phenomena at radio waves using high time resolution (5-100 ms).
First, the analog signal from the antenna (1000-2500 MHz) is sent to a spectrum analyzer (HP8559-A). After that, the analog signal is digitized during 5 minutes in a NI USB-6009 device connected to the PC, before to be stored in a file. By that time, other acquisition data cycle is restarted and so on up to the end of day.
However, we need timestamp (UTC) the solar data at the beginning and end of each sample of 5 milliseconds, during all acquisition process, in order to have the UTC time information of recorded solar events. So, a time resolution of at least 1 ms is required.
A software permit us to read recorded data and visualize corresponding spectra during last 5 minutes. However, we need UTC time information in the format hh:mm:ss.sss UT. Then, UTC millisecond is important for us, but not available yet.
To solve this problem, we are searching for a high accuracy timing GPS receiver (on the order of microseconds or nanoseconds), with at least three significant digits of precision (UT time in milliseconds) and which give us the UTC signal at least each 5 milliseconds or even better (1 ms). However, most GPS receivers only outputs 1 PPS (Pulse Per Second = 1000 millisecond).
Then, we are open to a better addressing on how to solve this problem !!
We know that GPS time synchronization with PXI-6608 can be used to precisely timestamp data acquisition, but we have to solve this problem with a lower cost. Also, we require a PCI interfacing instead of PXI.
Do we have to use a timer card? How do we use a timer, GPS and USB-6009 to timestamp data acquisition? Does the NI PCI-6602 solve the problem?
Obs:
The data acquisition software was developed in C++ Builder to run on a PC (Pentium III 2 GHz) under Windows XP environment. We used the NI-DAQmxBase driver to sample the signal from the NI USB-6009.
We are sure your expertise can help us on this matter.
Regards,

I better explain my problem in the thread How to timestamp continuous analog data acquisition using USB-6009 and GPS timing board?
We are considering to use the PCI-1588 or a GPS timing board (low-profile slot too), but I´m not sure that the USB-6009 can be used to solve the problem.
How to syncronize the data acquisition and timestamps using USB-6009 and PCI-1588 with external GPS?
In other thread I would appreciate any suggestions for GPS timing board and PCI-1588 too.
Regards,
Lilian

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